Starting phenix.real_space_refine on Fri Nov 15 01:12:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsp_60423/11_2024/8zsp_60423.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsp_60423/11_2024/8zsp_60423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsp_60423/11_2024/8zsp_60423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsp_60423/11_2024/8zsp_60423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsp_60423/11_2024/8zsp_60423.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsp_60423/11_2024/8zsp_60423.cif" } resolution = 3.14 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5129 2.51 5 N 1390 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1874 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2180 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'HIS:plan': 3, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.60 Number of scatterers: 8076 At special positions: 0 Unit cell: (73.216, 98.176, 132.288, 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 59 16.00 O 1498 8.00 N 1390 7.00 C 5129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.02 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 42.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.561A pdb=" N ALA A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.596A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.779A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 removed outlier: 4.050A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.239A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.515A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.337A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 23 through 51 Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 84 removed outlier: 3.799A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 127 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 188 through 199 removed outlier: 3.964A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 211 removed outlier: 3.534A pdb=" N TYR R 210 " --> pdb=" O MET R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 248 through 274 removed outlier: 3.880A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU R 261 " --> pdb=" O MET R 257 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.678A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 75 removed outlier: 10.034A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ASP A 111 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.698A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.890A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.812A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.707A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.979A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.813A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.435A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1209 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: 2.21 Time building geometry restraints manager: 2.54 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: 1321 1.31 - 1.44: 2298 1.44 - 1.56: 4544 1.56 - 1.69: 4 1.69 - 1.81: 84 Bond restraints: 8251 Sorted by residual: bond pdb=" C12 7LD R 401 " pdb=" N2 7LD R 401 " ideal model delta sigma weight residual 1.450 1.241 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C13 7LD R 401 " pdb=" N2 7LD R 401 " ideal model delta sigma weight residual 1.451 1.257 0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C10 7LD R 401 " pdb=" C9 7LD R 401 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C1 7LD R 401 " pdb=" C4 7LD R 401 " ideal model delta sigma weight residual 1.395 1.568 -0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 7LD R 401 " pdb=" C14 7LD R 401 " ideal model delta sigma weight residual 1.501 1.333 0.168 2.00e-02 2.50e+03 7.09e+01 ... (remaining 8246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 11048 2.77 - 5.54: 135 5.54 - 8.31: 6 8.31 - 11.08: 2 11.08 - 13.84: 1 Bond angle restraints: 11192 Sorted by residual: angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.59 98.75 13.84 1.22e+00 6.72e-01 1.29e+02 angle pdb=" C MET R 158 " pdb=" N ILE R 159 " pdb=" CA ILE R 159 " ideal model delta sigma weight residual 122.35 113.70 8.65 1.18e+00 7.18e-01 5.37e+01 angle pdb=" N ASP B 170 " pdb=" CA ASP B 170 " pdb=" C ASP B 170 " ideal model delta sigma weight residual 109.07 99.73 9.34 1.61e+00 3.86e-01 3.37e+01 angle pdb=" N PHE R 156 " pdb=" CA PHE R 156 " pdb=" C PHE R 156 " ideal model delta sigma weight residual 113.01 107.55 5.46 1.20e+00 6.94e-01 2.07e+01 angle pdb=" N LYS R 174 " pdb=" CA LYS R 174 " pdb=" C LYS R 174 " ideal model delta sigma weight residual 111.28 106.50 4.78 1.09e+00 8.42e-01 1.92e+01 ... (remaining 11187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 4758 31.11 - 62.22: 134 62.22 - 93.32: 14 93.32 - 124.43: 0 124.43 - 155.54: 1 Dihedral angle restraints: 4907 sinusoidal: 1900 harmonic: 3007 Sorted by residual: dihedral pdb=" C16 7LD R 401 " pdb=" C17 7LD R 401 " pdb=" N3 7LD R 401 " pdb=" C18 7LD R 401 " ideal model delta sinusoidal sigma weight residual 91.75 -112.71 -155.54 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CA ASP B 163 " pdb=" CB ASP B 163 " ideal model delta harmonic sigma weight residual 122.80 112.75 10.05 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CA ASN B 237 " pdb=" C ASN B 237 " pdb=" N GLY B 238 " pdb=" CA GLY B 238 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 983 0.055 - 0.109: 217 0.109 - 0.164: 51 0.164 - 0.218: 5 0.218 - 0.273: 2 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE R 171 " pdb=" N ILE R 171 " pdb=" C ILE R 171 " pdb=" CB ILE R 171 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL R 184 " pdb=" CA VAL R 184 " pdb=" CG1 VAL R 184 " pdb=" CG2 VAL R 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1255 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 152 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ALA R 152 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA R 152 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL R 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 236 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 130 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C ARG R 130 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG R 130 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR R 131 " 0.010 2.00e-02 2.50e+03 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1719 2.78 - 3.31: 8034 3.31 - 3.84: 13848 3.84 - 4.37: 16597 4.37 - 4.90: 28528 Nonbonded interactions: 68726 Sorted by model distance: nonbonded pdb=" O LEU R 295 " pdb=" OG1 THR R 298 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.271 3.040 nonbonded pdb=" O CYS B 148 " pdb=" OG SER B 160 " model vdw 2.275 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.283 3.040 ... (remaining 68721 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: 0.690 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.060 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.008 0.209 8251 Z= 0.541 Angle : 0.718 13.844 11192 Z= 0.459 Chirality : 0.049 0.273 1258 Planarity : 0.004 0.049 1427 Dihedral : 14.307 155.536 2954 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.12 % Allowed : 1.16 % Favored : 98.72 % 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: 0.24 (0.27), residues: 1019 helix: 1.53 (0.27), residues: 398 sheet: -0.58 (0.38), residues: 187 loop : -0.75 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.001 PHE B 234 TYR 0.011 0.001 TYR B 105 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.6839 (tp30) cc_final: 0.6610 (tp30) REVERT: A 166 GLU cc_start: 0.8085 (mp0) cc_final: 0.7797 (mp0) REVERT: B 10 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 86 THR cc_start: 0.8337 (p) cc_final: 0.7740 (p) REVERT: B 88 ASN cc_start: 0.7917 (m-40) cc_final: 0.7558 (m110) REVERT: B 118 ASP cc_start: 0.7322 (p0) cc_final: 0.7108 (p0) REVERT: B 163 ASP cc_start: 0.7550 (t0) cc_final: 0.7169 (t70) REVERT: B 189 SER cc_start: 0.8222 (t) cc_final: 0.7990 (p) REVERT: B 271 CYS cc_start: 0.7082 (m) cc_final: 0.6849 (m) REVERT: N 60 TYR cc_start: 0.8396 (m-80) cc_final: 0.7895 (m-80) REVERT: R 145 PHE cc_start: 0.7755 (t80) cc_final: 0.7463 (t80) REVERT: R 273 MET cc_start: 0.6544 (mtm) cc_final: 0.6212 (mtm) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2634 time to fit residues: 80.4163 Evaluate side-chains 211 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 146 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 31 ASN R 99 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8251 Z= 0.239 Angle : 0.559 7.696 11192 Z= 0.300 Chirality : 0.044 0.149 1258 Planarity : 0.004 0.042 1427 Dihedral : 6.514 138.672 1147 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.16 % Allowed : 12.76 % Favored : 86.08 % 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: 0.42 (0.26), residues: 1019 helix: 1.71 (0.26), residues: 397 sheet: -0.40 (0.36), residues: 190 loop : -0.71 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS R 113 PHE 0.016 0.002 PHE R 156 TYR 0.016 0.001 TYR A 115 ARG 0.006 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8102 (mp0) cc_final: 0.7819 (mp0) REVERT: A 177 THR cc_start: 0.8373 (m) cc_final: 0.7942 (p) REVERT: B 10 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 68 ARG cc_start: 0.7884 (ttt180) cc_final: 0.7581 (ttt180) REVERT: B 86 THR cc_start: 0.8475 (p) cc_final: 0.7925 (p) REVERT: B 88 ASN cc_start: 0.7996 (m-40) cc_final: 0.7610 (m110) REVERT: B 118 ASP cc_start: 0.7408 (p0) cc_final: 0.7201 (p0) REVERT: B 163 ASP cc_start: 0.6955 (t0) cc_final: 0.6727 (t70) REVERT: B 212 ASP cc_start: 0.7681 (t0) cc_final: 0.7277 (t0) REVERT: B 258 ASP cc_start: 0.8390 (t0) cc_final: 0.7904 (t0) REVERT: B 271 CYS cc_start: 0.7317 (m) cc_final: 0.7085 (m) REVERT: G 21 MET cc_start: 0.6552 (mmp) cc_final: 0.6282 (mmp) REVERT: N 60 TYR cc_start: 0.8299 (m-80) cc_final: 0.7937 (m-80) REVERT: R 43 ILE cc_start: 0.7924 (mt) cc_final: 0.7638 (mt) REVERT: R 273 MET cc_start: 0.6692 (mtm) cc_final: 0.6372 (mtm) outliers start: 10 outliers final: 2 residues processed: 237 average time/residue: 0.2434 time to fit residues: 74.9674 Evaluate side-chains 224 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 140 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 0.0040 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 : 0.003 0.034 8251 Z= 0.194 Angle : 0.521 8.507 11192 Z= 0.275 Chirality : 0.042 0.149 1258 Planarity : 0.004 0.044 1427 Dihedral : 5.843 120.510 1147 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.39 % Allowed : 14.97 % Favored : 83.64 % 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: 0.69 (0.26), residues: 1019 helix: 1.94 (0.26), residues: 401 sheet: -0.25 (0.35), residues: 199 loop : -0.59 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.006 0.001 HIS R 113 PHE 0.019 0.002 PHE A 228 TYR 0.017 0.001 TYR A 115 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8170 (mp0) cc_final: 0.7786 (mp0) REVERT: A 74 PHE cc_start: 0.7754 (p90) cc_final: 0.7395 (p90) REVERT: A 166 GLU cc_start: 0.8112 (mp0) cc_final: 0.7816 (mp0) REVERT: A 177 THR cc_start: 0.8341 (m) cc_final: 0.7929 (p) REVERT: B 10 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 86 THR cc_start: 0.8455 (p) cc_final: 0.7871 (p) REVERT: B 88 ASN cc_start: 0.7933 (m-40) cc_final: 0.7539 (m110) REVERT: B 118 ASP cc_start: 0.7439 (p0) cc_final: 0.7203 (p0) REVERT: B 163 ASP cc_start: 0.6999 (t0) cc_final: 0.6450 (t0) REVERT: B 212 ASP cc_start: 0.7668 (t0) cc_final: 0.7408 (t0) REVERT: B 247 ASP cc_start: 0.7233 (p0) cc_final: 0.6959 (p0) REVERT: B 271 CYS cc_start: 0.7204 (m) cc_final: 0.6997 (m) REVERT: B 290 ASP cc_start: 0.7628 (p0) cc_final: 0.7401 (p0) REVERT: G 21 MET cc_start: 0.6532 (mmp) cc_final: 0.6297 (mmp) REVERT: N 60 TYR cc_start: 0.8232 (m-80) cc_final: 0.7986 (m-80) REVERT: N 112 SER cc_start: 0.7815 (m) cc_final: 0.7509 (m) REVERT: R 273 MET cc_start: 0.6712 (mtm) cc_final: 0.6432 (mtm) outliers start: 12 outliers final: 10 residues processed: 243 average time/residue: 0.2293 time to fit residues: 73.8252 Evaluate side-chains 246 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 302 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8251 Z= 0.210 Angle : 0.524 9.148 11192 Z= 0.274 Chirality : 0.043 0.207 1258 Planarity : 0.004 0.045 1427 Dihedral : 5.364 100.275 1147 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 16.82 % Favored : 81.32 % 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: 0.73 (0.27), residues: 1019 helix: 1.98 (0.26), residues: 401 sheet: -0.33 (0.35), residues: 201 loop : -0.52 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.005 0.001 HIS R 113 PHE 0.028 0.002 PHE R 185 TYR 0.017 0.001 TYR A 115 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.856 Fit side-chains REVERT: A 14 GLU cc_start: 0.8173 (mp0) cc_final: 0.7771 (mp0) REVERT: A 24 MET cc_start: 0.7665 (tmm) cc_final: 0.7323 (tmm) REVERT: A 74 PHE cc_start: 0.7754 (p90) cc_final: 0.7421 (p90) REVERT: A 166 GLU cc_start: 0.8104 (mp0) cc_final: 0.7831 (mp0) REVERT: A 177 THR cc_start: 0.8390 (m) cc_final: 0.7983 (p) REVERT: B 86 THR cc_start: 0.8411 (p) cc_final: 0.7820 (p) REVERT: B 88 ASN cc_start: 0.7929 (m-40) cc_final: 0.7531 (m-40) REVERT: B 118 ASP cc_start: 0.7425 (p0) cc_final: 0.7206 (p0) REVERT: B 163 ASP cc_start: 0.6963 (t0) cc_final: 0.6405 (t0) REVERT: B 212 ASP cc_start: 0.7669 (t0) cc_final: 0.7389 (t0) REVERT: B 258 ASP cc_start: 0.8417 (t0) cc_final: 0.8138 (t0) REVERT: B 271 CYS cc_start: 0.7205 (m) cc_final: 0.6972 (m) REVERT: G 21 MET cc_start: 0.6525 (mmp) cc_final: 0.6262 (mmp) REVERT: N 60 TYR cc_start: 0.8197 (m-80) cc_final: 0.7996 (m-80) REVERT: R 273 MET cc_start: 0.6764 (mtm) cc_final: 0.6517 (mtm) outliers start: 16 outliers final: 12 residues processed: 247 average time/residue: 0.2411 time to fit residues: 77.2111 Evaluate side-chains 247 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 235 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain R residue 302 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8251 Z= 0.327 Angle : 0.580 10.351 11192 Z= 0.304 Chirality : 0.045 0.226 1258 Planarity : 0.004 0.044 1427 Dihedral : 5.229 86.312 1147 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 18.45 % Favored : 79.12 % 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: 0.60 (0.26), residues: 1019 helix: 1.86 (0.26), residues: 394 sheet: -0.31 (0.34), residues: 200 loop : -0.59 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.027 0.002 PHE R 185 TYR 0.022 0.002 TYR A 115 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8187 (mp0) cc_final: 0.7795 (mp0) REVERT: A 24 MET cc_start: 0.7711 (tmm) cc_final: 0.7348 (tmm) REVERT: A 74 PHE cc_start: 0.7738 (p90) cc_final: 0.7501 (p90) REVERT: A 166 GLU cc_start: 0.8114 (mp0) cc_final: 0.7816 (mp0) REVERT: A 177 THR cc_start: 0.8363 (m) cc_final: 0.7957 (p) REVERT: B 83 ASP cc_start: 0.8267 (t0) cc_final: 0.8014 (t70) REVERT: B 86 THR cc_start: 0.8389 (p) cc_final: 0.7741 (p) REVERT: B 88 ASN cc_start: 0.7960 (m-40) cc_final: 0.7511 (m-40) REVERT: B 102 THR cc_start: 0.7918 (t) cc_final: 0.7709 (t) REVERT: B 118 ASP cc_start: 0.7396 (p0) cc_final: 0.7174 (p0) REVERT: B 163 ASP cc_start: 0.6958 (t0) cc_final: 0.6386 (t0) REVERT: B 212 ASP cc_start: 0.7662 (t0) cc_final: 0.7377 (t0) REVERT: B 258 ASP cc_start: 0.8436 (t0) cc_final: 0.8085 (t0) REVERT: G 21 MET cc_start: 0.6548 (mmp) cc_final: 0.6301 (mmp) REVERT: N 60 TYR cc_start: 0.8201 (m-80) cc_final: 0.7902 (m-80) REVERT: R 71 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6940 (mp) REVERT: R 273 MET cc_start: 0.6857 (mtm) cc_final: 0.6648 (mtm) outliers start: 21 outliers final: 14 residues processed: 236 average time/residue: 0.2437 time to fit residues: 74.4396 Evaluate side-chains 239 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8251 Z= 0.190 Angle : 0.563 13.716 11192 Z= 0.283 Chirality : 0.044 0.400 1258 Planarity : 0.004 0.044 1427 Dihedral : 4.655 64.379 1147 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.74 % Allowed : 19.37 % Favored : 78.89 % 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: 0.72 (0.26), residues: 1019 helix: 1.93 (0.26), residues: 400 sheet: -0.36 (0.34), residues: 201 loop : -0.47 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS R 113 PHE 0.026 0.001 PHE R 185 TYR 0.025 0.001 TYR N 115 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8175 (mp0) cc_final: 0.7817 (mp0) REVERT: A 74 PHE cc_start: 0.7673 (p90) cc_final: 0.7319 (p90) REVERT: A 83 MET cc_start: 0.7894 (mtp) cc_final: 0.7661 (mtm) REVERT: A 166 GLU cc_start: 0.8105 (mp0) cc_final: 0.7814 (mp0) REVERT: A 170 TYR cc_start: 0.8258 (t80) cc_final: 0.7311 (t80) REVERT: A 177 THR cc_start: 0.8339 (m) cc_final: 0.7935 (p) REVERT: A 228 PHE cc_start: 0.8381 (t80) cc_final: 0.8160 (t80) REVERT: B 86 THR cc_start: 0.8360 (p) cc_final: 0.7701 (p) REVERT: B 88 ASN cc_start: 0.7924 (m-40) cc_final: 0.7514 (m110) REVERT: B 118 ASP cc_start: 0.7359 (p0) cc_final: 0.7116 (p0) REVERT: B 163 ASP cc_start: 0.6928 (t0) cc_final: 0.6383 (t0) REVERT: B 212 ASP cc_start: 0.7626 (t0) cc_final: 0.7357 (t0) REVERT: B 251 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7088 (ttm170) REVERT: B 258 ASP cc_start: 0.8428 (t0) cc_final: 0.8082 (t0) REVERT: G 21 MET cc_start: 0.6503 (mmp) cc_final: 0.6246 (mmp) REVERT: N 112 SER cc_start: 0.7793 (m) cc_final: 0.7403 (m) REVERT: R 273 MET cc_start: 0.6799 (mtm) cc_final: 0.6585 (mtm) outliers start: 15 outliers final: 11 residues processed: 235 average time/residue: 0.2416 time to fit residues: 73.6200 Evaluate side-chains 232 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8251 Z= 0.176 Angle : 0.546 13.151 11192 Z= 0.278 Chirality : 0.043 0.234 1258 Planarity : 0.004 0.046 1427 Dihedral : 4.355 48.726 1147 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.09 % Allowed : 20.07 % Favored : 77.84 % 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: 0.80 (0.27), residues: 1019 helix: 2.08 (0.26), residues: 394 sheet: -0.38 (0.34), residues: 201 loop : -0.44 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS R 113 PHE 0.023 0.001 PHE B 241 TYR 0.023 0.001 TYR N 115 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.925 Fit side-chains REVERT: A 14 GLU cc_start: 0.8180 (mp0) cc_final: 0.7866 (mp0) REVERT: A 74 PHE cc_start: 0.7683 (p90) cc_final: 0.7360 (p90) REVERT: A 83 MET cc_start: 0.7894 (mtp) cc_final: 0.7664 (mtm) REVERT: A 166 GLU cc_start: 0.8091 (mp0) cc_final: 0.7801 (mp0) REVERT: A 177 THR cc_start: 0.8319 (m) cc_final: 0.7935 (p) REVERT: A 228 PHE cc_start: 0.8369 (t80) cc_final: 0.8168 (t80) REVERT: B 86 THR cc_start: 0.8328 (p) cc_final: 0.7705 (p) REVERT: B 88 ASN cc_start: 0.7895 (m-40) cc_final: 0.7477 (m110) REVERT: B 118 ASP cc_start: 0.7328 (p0) cc_final: 0.7098 (p0) REVERT: B 163 ASP cc_start: 0.6936 (t0) cc_final: 0.6397 (t0) REVERT: B 212 ASP cc_start: 0.7615 (t0) cc_final: 0.7342 (t0) REVERT: B 258 ASP cc_start: 0.8404 (t0) cc_final: 0.8062 (t0) REVERT: G 21 MET cc_start: 0.6510 (mmp) cc_final: 0.6252 (mmp) REVERT: N 60 TYR cc_start: 0.8167 (m-80) cc_final: 0.7936 (m-80) REVERT: N 112 SER cc_start: 0.7841 (m) cc_final: 0.7495 (m) REVERT: R 43 ILE cc_start: 0.7937 (mt) cc_final: 0.7693 (mt) REVERT: R 161 LEU cc_start: 0.8103 (mt) cc_final: 0.7849 (mp) REVERT: R 273 MET cc_start: 0.6794 (mtm) cc_final: 0.6576 (mtm) outliers start: 18 outliers final: 11 residues processed: 231 average time/residue: 0.2425 time to fit residues: 72.4732 Evaluate side-chains 231 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8251 Z= 0.198 Angle : 0.553 12.764 11192 Z= 0.281 Chirality : 0.043 0.238 1258 Planarity : 0.004 0.046 1427 Dihedral : 4.195 35.642 1147 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.74 % Allowed : 21.46 % Favored : 76.80 % 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: 0.76 (0.26), residues: 1019 helix: 2.07 (0.26), residues: 394 sheet: -0.44 (0.34), residues: 203 loop : -0.46 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS R 113 PHE 0.024 0.001 PHE B 241 TYR 0.021 0.001 TYR N 115 ARG 0.008 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 0.806 Fit side-chains REVERT: A 14 GLU cc_start: 0.8192 (mp0) cc_final: 0.7885 (mp0) REVERT: A 74 PHE cc_start: 0.7692 (p90) cc_final: 0.7369 (p90) REVERT: A 83 MET cc_start: 0.7917 (mtp) cc_final: 0.7688 (mtm) REVERT: A 166 GLU cc_start: 0.8079 (mp0) cc_final: 0.7807 (mp0) REVERT: A 177 THR cc_start: 0.8322 (m) cc_final: 0.7938 (p) REVERT: B 86 THR cc_start: 0.8342 (p) cc_final: 0.7720 (p) REVERT: B 88 ASN cc_start: 0.7885 (m-40) cc_final: 0.7480 (m110) REVERT: B 118 ASP cc_start: 0.7315 (p0) cc_final: 0.7099 (p0) REVERT: B 163 ASP cc_start: 0.6943 (t0) cc_final: 0.6408 (t0) REVERT: B 212 ASP cc_start: 0.7645 (t0) cc_final: 0.7352 (t0) REVERT: B 258 ASP cc_start: 0.8396 (t0) cc_final: 0.8067 (t0) REVERT: G 21 MET cc_start: 0.6515 (mmp) cc_final: 0.6257 (mmp) REVERT: N 60 TYR cc_start: 0.8160 (m-80) cc_final: 0.7920 (m-80) REVERT: N 112 SER cc_start: 0.7854 (m) cc_final: 0.7497 (m) REVERT: R 43 ILE cc_start: 0.7936 (mt) cc_final: 0.7689 (mt) REVERT: R 273 MET cc_start: 0.6835 (mtm) cc_final: 0.6618 (mtm) outliers start: 15 outliers final: 11 residues processed: 222 average time/residue: 0.2272 time to fit residues: 65.9112 Evaluate side-chains 227 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 302 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8251 Z= 0.226 Angle : 0.568 9.483 11192 Z= 0.291 Chirality : 0.044 0.249 1258 Planarity : 0.004 0.046 1427 Dihedral : 4.179 37.694 1147 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.97 % Allowed : 21.35 % Favored : 76.68 % 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: 0.75 (0.26), residues: 1019 helix: 2.04 (0.26), residues: 394 sheet: -0.34 (0.34), residues: 195 loop : -0.52 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 113 PHE 0.026 0.002 PHE B 241 TYR 0.020 0.001 TYR N 115 ARG 0.010 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.980 Fit side-chains REVERT: A 14 GLU cc_start: 0.8191 (mp0) cc_final: 0.7887 (mp0) REVERT: A 74 PHE cc_start: 0.7687 (p90) cc_final: 0.7374 (p90) REVERT: A 83 MET cc_start: 0.7938 (mtp) cc_final: 0.7717 (mtm) REVERT: A 161 GLU cc_start: 0.6661 (pm20) cc_final: 0.6319 (pm20) REVERT: A 166 GLU cc_start: 0.8078 (mp0) cc_final: 0.7807 (mp0) REVERT: A 177 THR cc_start: 0.8339 (m) cc_final: 0.7952 (p) REVERT: B 86 THR cc_start: 0.8334 (p) cc_final: 0.7743 (p) REVERT: B 88 ASN cc_start: 0.7886 (m-40) cc_final: 0.7519 (m110) REVERT: B 118 ASP cc_start: 0.7316 (p0) cc_final: 0.7093 (p0) REVERT: B 163 ASP cc_start: 0.6938 (t0) cc_final: 0.6390 (t0) REVERT: B 212 ASP cc_start: 0.7630 (t0) cc_final: 0.7334 (t0) REVERT: B 258 ASP cc_start: 0.8378 (t0) cc_final: 0.8042 (t0) REVERT: G 21 MET cc_start: 0.6529 (mmp) cc_final: 0.6249 (mmp) REVERT: N 60 TYR cc_start: 0.8164 (m-80) cc_final: 0.7927 (m-80) REVERT: N 112 SER cc_start: 0.7871 (m) cc_final: 0.7527 (m) REVERT: R 43 ILE cc_start: 0.7947 (mt) cc_final: 0.7685 (mt) REVERT: R 55 HIS cc_start: 0.7943 (m90) cc_final: 0.7664 (m90) REVERT: R 257 MET cc_start: 0.6572 (tpp) cc_final: 0.6323 (tpp) REVERT: R 273 MET cc_start: 0.6832 (mtm) cc_final: 0.6630 (mtm) outliers start: 17 outliers final: 12 residues processed: 230 average time/residue: 0.2309 time to fit residues: 69.9179 Evaluate side-chains 236 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 302 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 61 optimal weight: 0.0170 chunk 49 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8251 Z= 0.155 Angle : 0.559 12.908 11192 Z= 0.284 Chirality : 0.043 0.232 1258 Planarity : 0.004 0.046 1427 Dihedral : 4.047 40.874 1147 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.51 % Allowed : 22.74 % Favored : 75.75 % 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: 0.84 (0.26), residues: 1019 helix: 2.15 (0.26), residues: 394 sheet: -0.29 (0.34), residues: 195 loop : -0.51 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 63 HIS 0.005 0.001 HIS R 113 PHE 0.026 0.001 PHE B 241 TYR 0.019 0.001 TYR N 115 ARG 0.006 0.000 ARG A 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.891 Fit side-chains REVERT: A 14 GLU cc_start: 0.8188 (mp0) cc_final: 0.7933 (mp0) REVERT: A 166 GLU cc_start: 0.8042 (mp0) cc_final: 0.7768 (mp0) REVERT: A 177 THR cc_start: 0.8315 (m) cc_final: 0.7942 (p) REVERT: A 216 THR cc_start: 0.8103 (m) cc_final: 0.7820 (p) REVERT: B 50 THR cc_start: 0.7816 (m) cc_final: 0.7571 (p) REVERT: B 86 THR cc_start: 0.8312 (p) cc_final: 0.7713 (p) REVERT: B 88 ASN cc_start: 0.7836 (m-40) cc_final: 0.7463 (m110) REVERT: B 93 ILE cc_start: 0.8161 (mp) cc_final: 0.7831 (mp) REVERT: B 118 ASP cc_start: 0.7283 (p0) cc_final: 0.7070 (p0) REVERT: B 163 ASP cc_start: 0.6875 (t0) cc_final: 0.6379 (t0) REVERT: B 212 ASP cc_start: 0.7624 (t0) cc_final: 0.7333 (t0) REVERT: B 247 ASP cc_start: 0.7453 (p0) cc_final: 0.7179 (p0) REVERT: B 258 ASP cc_start: 0.8353 (t0) cc_final: 0.8007 (t0) REVERT: G 21 MET cc_start: 0.6479 (mmp) cc_final: 0.6206 (mmp) REVERT: N 112 SER cc_start: 0.7823 (m) cc_final: 0.7471 (m) REVERT: R 43 ILE cc_start: 0.7898 (mt) cc_final: 0.7628 (mt) REVERT: R 76 VAL cc_start: 0.7173 (m) cc_final: 0.6761 (p) REVERT: R 273 MET cc_start: 0.6763 (mtm) cc_final: 0.6550 (mtm) outliers start: 13 outliers final: 11 residues processed: 224 average time/residue: 0.2277 time to fit residues: 67.0374 Evaluate side-chains 224 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 302 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 239 ASN ** B 259 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 = 0.3794 r_free = 0.3794 target = 0.136407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119690 restraints weight = 11833.279| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.34 r_work: 0.3454 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8251 Z= 0.323 Angle : 0.602 9.752 11192 Z= 0.314 Chirality : 0.046 0.266 1258 Planarity : 0.004 0.046 1427 Dihedral : 4.244 42.771 1147 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.74 % Allowed : 23.20 % Favored : 75.06 % 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: 0.59 (0.26), residues: 1019 helix: 1.95 (0.26), residues: 394 sheet: -0.55 (0.34), residues: 199 loop : -0.57 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP B 63 HIS 0.005 0.001 HIS R 113 PHE 0.026 0.002 PHE B 241 TYR 0.020 0.002 TYR N 60 ARG 0.007 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.40 seconds wall clock time: 43 minutes 20.11 seconds (2600.11 seconds total)