Starting phenix.real_space_refine on Tue Sep 24 05:42:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/09_2024/8iq4_35657.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/09_2024/8iq4_35657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/09_2024/8iq4_35657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/09_2024/8iq4_35657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/09_2024/8iq4_35657.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/09_2024/8iq4_35657.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4555 2.51 5 N 1208 2.21 5 O 1265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7080 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1564 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2342 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 238 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 845 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'87Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.65 Number of scatterers: 7080 At special positions: 0 Unit cell: (70.2656, 96.6152, 124.063, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1265 8.00 N 1208 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 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 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 40.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'R' and resid 29 through 60 removed outlier: 4.471A pdb=" N SER R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 105 through 139 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 147 through 173 removed outlier: 4.164A pdb=" N HIS R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 229 removed outlier: 4.018A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 275 Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.826A pdb=" N PHE R 288 " --> pdb=" O GLU R 284 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 313 Processing helix chain 'A' and resid 18 through 39 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.532A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.759A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 16 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 179 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.721A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.472A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.746A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.450A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.550A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.575A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1173 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: 2.22 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2261 1.34 - 1.46: 1812 1.46 - 1.58: 3078 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 7222 Sorted by residual: bond pdb=" C13 87Q R 401 " pdb=" C14 87Q R 401 " ideal model delta sigma weight residual 1.499 1.563 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C10 87Q R 401 " pdb=" C11 87Q R 401 " ideal model delta sigma weight residual 1.490 1.540 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" C15 87Q R 401 " pdb=" C16 87Q R 401 " ideal model delta sigma weight residual 1.500 1.546 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C06 87Q R 401 " pdb=" C09 87Q R 401 " ideal model delta sigma weight residual 1.505 1.542 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" C06 87Q R 401 " pdb=" O08 87Q R 401 " ideal model delta sigma weight residual 1.426 1.391 0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 7217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 9818 5.18 - 10.36: 6 10.36 - 15.55: 2 15.55 - 20.73: 0 20.73 - 25.91: 1 Bond angle restraints: 9827 Sorted by residual: angle pdb=" C09 87Q R 401 " pdb=" C10 87Q R 401 " pdb=" C11 87Q R 401 " ideal model delta sigma weight residual 124.44 150.35 -25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" C13 87Q R 401 " pdb=" C14 87Q R 401 " pdb=" C15 87Q R 401 " ideal model delta sigma weight residual 126.67 114.18 12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C06 87Q R 401 " pdb=" C09 87Q R 401 " pdb=" C10 87Q R 401 " ideal model delta sigma weight residual 127.22 114.91 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C ARG R 59 " pdb=" N GLN R 60 " pdb=" CA GLN R 60 " ideal model delta sigma weight residual 122.31 115.55 6.76 1.81e+00 3.05e-01 1.40e+01 angle pdb=" C14 87Q R 401 " pdb=" C15 87Q R 401 " pdb=" C16 87Q R 401 " ideal model delta sigma weight residual 126.41 117.48 8.93 3.00e+00 1.11e-01 8.86e+00 ... (remaining 9822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3777 17.81 - 35.62: 337 35.62 - 53.44: 83 53.44 - 71.25: 17 71.25 - 89.06: 5 Dihedral angle restraints: 4219 sinusoidal: 1453 harmonic: 2766 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -121.49 35.49 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA ARG R 100 " pdb=" C ARG R 100 " pdb=" N PHE R 101 " pdb=" CA PHE R 101 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" SG CYS N 99 " pdb=" CB CYS N 107 " pdb=" SG CYS N 107 " pdb=" CA CYS N 107 " ideal model delta sinusoidal sigma weight residual -73.00 -1.88 -71.12 1 2.00e+01 2.50e-03 1.62e+01 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1098 0.082 - 0.163: 68 0.163 - 0.244: 2 0.244 - 0.326: 1 0.326 - 0.407: 1 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C12 87Q R 401 " pdb=" C11 87Q R 401 " pdb=" C13 87Q R 401 " pdb=" C22 87Q R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.94 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C11 87Q R 401 " pdb=" C10 87Q R 401 " pdb=" C12 87Q R 401 " pdb=" C25 87Q R 401 " both_signs ideal model delta sigma weight residual False 2.63 2.92 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C06 87Q R 401 " pdb=" C05 87Q R 401 " pdb=" C07 87Q R 401 " pdb=" C09 87Q R 401 " both_signs ideal model delta sigma weight residual False -2.54 -2.75 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1167 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 263 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO R 264 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 264 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 264 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 236 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C THR B 87 " 0.028 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.010 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 945 2.75 - 3.29: 6525 3.29 - 3.83: 11972 3.83 - 4.36: 14102 4.36 - 4.90: 25373 Nonbonded interactions: 58917 Sorted by model distance: nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD2 ASP B 163 " model vdw 2.269 3.040 ... (remaining 58912 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: 2.870 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.230 Find NCS groups from input model: 0.070 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7222 Z= 0.202 Angle : 0.603 25.912 9827 Z= 0.294 Chirality : 0.043 0.407 1170 Planarity : 0.003 0.047 1225 Dihedral : 14.910 89.058 2416 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.58 % Allowed : 12.77 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 930 helix: 3.05 (0.26), residues: 340 sheet: 1.05 (0.35), residues: 206 loop : -1.16 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.838 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 1.1192 time to fit residues: 117.5018 Evaluate side-chains 98 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 365 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 ASN B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7222 Z= 0.290 Angle : 0.551 6.745 9827 Z= 0.303 Chirality : 0.043 0.153 1170 Planarity : 0.004 0.051 1225 Dihedral : 6.156 83.602 1052 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.47 % Allowed : 12.63 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 930 helix: 2.96 (0.26), residues: 343 sheet: 0.92 (0.34), residues: 213 loop : -1.17 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.009 0.001 HIS A 357 PHE 0.018 0.002 PHE R 101 TYR 0.015 0.002 TYR B 105 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.886 Fit side-chains REVERT: B 219 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: B 234 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8513 (t80) REVERT: N 95 TYR cc_start: 0.8836 (m-80) cc_final: 0.8586 (m-80) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 1.1117 time to fit residues: 130.0951 Evaluate side-chains 109 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7222 Z= 0.196 Angle : 0.492 6.499 9827 Z= 0.274 Chirality : 0.041 0.149 1170 Planarity : 0.004 0.051 1225 Dihedral : 5.808 89.358 1050 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.32 % Allowed : 14.08 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 930 helix: 3.08 (0.26), residues: 344 sheet: 1.00 (0.33), residues: 212 loop : -1.24 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.735 Fit side-chains REVERT: B 219 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7647 (mtp180) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8448 (t80) REVERT: N 95 TYR cc_start: 0.8772 (m-80) cc_final: 0.8555 (m-80) outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 1.0116 time to fit residues: 118.5653 Evaluate side-chains 109 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.0030 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7222 Z= 0.155 Angle : 0.473 8.661 9827 Z= 0.260 Chirality : 0.040 0.147 1170 Planarity : 0.003 0.049 1225 Dihedral : 5.549 86.339 1050 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.89 % Allowed : 14.95 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 930 helix: 3.21 (0.26), residues: 344 sheet: 1.02 (0.33), residues: 212 loop : -1.21 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.786 Fit side-chains REVERT: B 219 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: B 234 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8357 (t80) REVERT: N 38 ARG cc_start: 0.8820 (ptt180) cc_final: 0.8445 (ptt180) REVERT: N 95 TYR cc_start: 0.8742 (m-80) cc_final: 0.8527 (m-80) outliers start: 13 outliers final: 9 residues processed: 116 average time/residue: 1.0252 time to fit residues: 126.5016 Evaluate side-chains 112 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain R residue 260 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7222 Z= 0.234 Angle : 0.512 6.595 9827 Z= 0.283 Chirality : 0.041 0.153 1170 Planarity : 0.004 0.051 1225 Dihedral : 5.769 89.077 1050 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.47 % Allowed : 15.24 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 930 helix: 3.08 (0.26), residues: 343 sheet: 0.91 (0.33), residues: 214 loop : -1.22 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE R 165 TYR 0.014 0.001 TYR A 358 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.802 Fit side-chains REVERT: B 219 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7264 (mmp-170) REVERT: B 234 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8531 (t80) REVERT: N 95 TYR cc_start: 0.8825 (m-80) cc_final: 0.8550 (m-80) outliers start: 17 outliers final: 11 residues processed: 110 average time/residue: 0.9870 time to fit residues: 116.0188 Evaluate side-chains 110 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7222 Z= 0.342 Angle : 0.590 8.830 9827 Z= 0.320 Chirality : 0.044 0.166 1170 Planarity : 0.004 0.055 1225 Dihedral : 6.014 81.269 1050 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.34 % Allowed : 14.51 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 930 helix: 2.76 (0.26), residues: 347 sheet: 0.74 (0.33), residues: 218 loop : -1.35 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.009 0.001 HIS A 357 PHE 0.019 0.002 PHE R 165 TYR 0.018 0.002 TYR A 358 ARG 0.004 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.703 Fit side-chains REVERT: B 219 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7335 (mmp-170) REVERT: B 234 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8657 (t80) REVERT: N 95 TYR cc_start: 0.8837 (m-80) cc_final: 0.8598 (m-80) outliers start: 23 outliers final: 14 residues processed: 113 average time/residue: 0.9717 time to fit residues: 117.2742 Evaluate side-chains 112 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7222 Z= 0.184 Angle : 0.489 6.616 9827 Z= 0.273 Chirality : 0.041 0.158 1170 Planarity : 0.004 0.053 1225 Dihedral : 5.697 89.842 1050 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.90 % Allowed : 15.53 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.27), residues: 930 helix: 3.04 (0.26), residues: 343 sheet: 1.00 (0.34), residues: 212 loop : -1.28 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.814 Fit side-chains REVERT: B 219 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7296 (mmp-170) REVERT: B 234 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8454 (t80) REVERT: N 38 ARG cc_start: 0.8837 (ptt180) cc_final: 0.8423 (ptt180) REVERT: N 95 TYR cc_start: 0.8789 (m-80) cc_final: 0.8532 (m-80) outliers start: 20 outliers final: 13 residues processed: 116 average time/residue: 0.9267 time to fit residues: 115.0200 Evaluate side-chains 117 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7222 Z= 0.160 Angle : 0.481 9.623 9827 Z= 0.263 Chirality : 0.040 0.160 1170 Planarity : 0.003 0.051 1225 Dihedral : 5.513 88.117 1050 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.32 % Allowed : 16.55 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 930 helix: 3.00 (0.26), residues: 350 sheet: 1.08 (0.34), residues: 212 loop : -1.26 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.739 Fit side-chains REVERT: B 219 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7633 (mtp180) REVERT: B 234 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8355 (t80) REVERT: N 95 TYR cc_start: 0.8758 (m-80) cc_final: 0.8526 (m-80) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.0138 time to fit residues: 125.2708 Evaluate side-chains 118 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain R residue 260 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7222 Z= 0.215 Angle : 0.504 6.700 9827 Z= 0.278 Chirality : 0.041 0.162 1170 Planarity : 0.004 0.053 1225 Dihedral : 5.648 86.524 1050 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 16.26 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 930 helix: 3.00 (0.26), residues: 346 sheet: 0.99 (0.34), residues: 214 loop : -1.28 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 165 TYR 0.013 0.001 TYR A 358 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.751 Fit side-chains REVERT: B 219 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7316 (mmp-170) REVERT: B 234 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8408 (t80) REVERT: N 95 TYR cc_start: 0.8816 (m-80) cc_final: 0.8556 (m-80) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.9994 time to fit residues: 123.8953 Evaluate side-chains 117 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7222 Z= 0.169 Angle : 0.490 9.772 9827 Z= 0.267 Chirality : 0.040 0.160 1170 Planarity : 0.003 0.052 1225 Dihedral : 5.532 87.928 1050 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.18 % Allowed : 16.69 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 930 helix: 3.06 (0.25), residues: 346 sheet: 1.10 (0.34), residues: 213 loop : -1.27 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.718 Fit side-chains REVERT: B 219 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: B 234 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8391 (t80) REVERT: N 38 ARG cc_start: 0.8834 (ptt180) cc_final: 0.8436 (ptt180) REVERT: N 95 TYR cc_start: 0.8758 (m-80) cc_final: 0.8522 (m-80) outliers start: 15 outliers final: 12 residues processed: 117 average time/residue: 1.0671 time to fit residues: 133.2820 Evaluate side-chains 120 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain R residue 260 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114094 restraints weight = 7643.964| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.41 r_work: 0.3186 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7222 Z= 0.189 Angle : 0.493 6.655 9827 Z= 0.273 Chirality : 0.041 0.162 1170 Planarity : 0.004 0.052 1225 Dihedral : 5.545 86.013 1050 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.47 % Allowed : 16.40 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 930 helix: 3.02 (0.25), residues: 346 sheet: 1.08 (0.34), residues: 213 loop : -1.30 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 165 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.98 seconds wall clock time: 48 minutes 57.44 seconds (2937.44 seconds total)