Starting phenix.real_space_refine on Thu Jul 2 10:25:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i7v_35234/07_2026/8i7v_35234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i7v_35234/07_2026/8i7v_35234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i7v_35234/07_2026/8i7v_35234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i7v_35234/07_2026/8i7v_35234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i7v_35234/07_2026/8i7v_35234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i7v_35234/07_2026/8i7v_35234.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.075 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 62 5.16 5 C 5345 2.51 5 N 1434 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8374 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2369 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1152 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'TRANS': 144} Chain breaks: 3 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8374 At special positions: 0 Unit cell: (89.64, 118.275, 129.48, 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 62 16.00 O 1533 8.00 N 1434 7.00 C 5345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 0.43 Conformation dependent library (CDL) restraints added in 265.8 milliseconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 35.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 29 through 54 Processing helix chain 'A' and resid 61 through 89 removed outlier: 3.527A pdb=" N PHE A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.904A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.772A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.558A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.913A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.043A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 53 removed outlier: 4.010A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.954A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 352 removed outlier: 4.142A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.613A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.227A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.936A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 4.077A pdb=" N ILE A 182 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 4.361A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.445A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.843A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.799A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS C 121 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.511A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.561A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.499A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.721A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.501A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.672A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.560A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.989A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1179 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: 1.00 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1344 1.31 - 1.45: 2417 1.45 - 1.58: 4702 1.58 - 1.71: 1 1.71 - 1.84: 90 Bond restraints: 8554 Sorted by residual: bond pdb=" C THR B 340 " pdb=" O THR B 340 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.15e-02 7.56e+03 2.40e+01 bond pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 1.237 1.192 0.046 1.16e-02 7.43e+03 1.54e+01 bond pdb=" C06 OJX A 401 " pdb=" N04 OJX A 401 " ideal model delta sigma weight residual 1.382 1.318 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N ILE B 343 " pdb=" CA ILE B 343 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.94e+00 bond pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 7.00e+00 ... (remaining 8549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11256 1.64 - 3.27: 249 3.27 - 4.91: 48 4.91 - 6.54: 17 6.54 - 8.18: 6 Bond angle restraints: 11576 Sorted by residual: angle pdb=" CA PRO E 75 " pdb=" N PRO E 75 " pdb=" CD PRO E 75 " ideal model delta sigma weight residual 112.00 103.92 8.08 1.40e+00 5.10e-01 3.33e+01 angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 108.66 5.05 9.50e-01 1.11e+00 2.83e+01 angle pdb=" CA PHE B 354 " pdb=" CB PHE B 354 " pdb=" CG PHE B 354 " ideal model delta sigma weight residual 113.80 118.66 -4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" CA THR B 340 " pdb=" C THR B 340 " pdb=" O THR B 340 " ideal model delta sigma weight residual 120.82 115.75 5.07 1.05e+00 9.07e-01 2.33e+01 angle pdb=" CA MET B 53 " pdb=" CB MET B 53 " pdb=" CG MET B 53 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 ... (remaining 11571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4393 17.20 - 34.40: 492 34.40 - 51.60: 141 51.60 - 68.80: 21 68.80 - 85.99: 9 Dihedral angle restraints: 5056 sinusoidal: 1981 harmonic: 3075 Sorted by residual: dihedral pdb=" CA MET A 167 " pdb=" C MET A 167 " pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE A 197 " pdb=" C PHE A 197 " pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta harmonic sigma weight residual 180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 266 " pdb=" CB CYS A 266 " ideal model delta sinusoidal sigma weight residual -86.00 -54.87 -31.13 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 5053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1115 0.060 - 0.120: 177 0.120 - 0.180: 13 0.180 - 0.240: 2 0.240 - 0.299: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CA ILE B 344 " pdb=" N ILE B 344 " pdb=" C ILE B 344 " pdb=" CB ILE B 344 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA MET B 53 " pdb=" N MET B 53 " pdb=" C MET B 53 " pdb=" CB MET B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU B 353 " pdb=" N LEU B 353 " pdb=" C LEU B 353 " pdb=" CB LEU B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1305 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO E 75 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO A 31 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 236 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.026 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 1426 2.77 - 3.48: 11302 3.48 - 4.19: 20174 4.19 - 4.90: 36798 Nonbonded interactions: 69702 Sorted by model distance: nonbonded pdb=" O PRO A 299 " pdb=" O PHE B 354 " model vdw 1.346 3.040 nonbonded pdb=" O LYS A 57 " pdb=" OD2 ASP C 312 " model vdw 1.899 3.040 nonbonded pdb=" O PRO A 299 " pdb=" C PHE B 354 " model vdw 2.143 3.270 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.185 3.040 nonbonded pdb=" O HIS B 213 " pdb=" OH TYR C 59 " model vdw 2.191 3.040 ... (remaining 69697 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: 0.430 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.004 0.110 8560 Z= 0.198 Angle : 0.640 8.178 11588 Z= 0.367 Chirality : 0.044 0.299 1308 Planarity : 0.005 0.117 1460 Dihedral : 16.041 85.994 3050 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 1.76 % Allowed : 18.33 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1048 helix: 1.65 (0.28), residues: 331 sheet: 0.64 (0.30), residues: 291 loop : -0.48 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.012 0.001 TYR E 103 PHE 0.020 0.001 PHE B 354 TRP 0.025 0.002 TRP A 256 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.20 ( 8554) covalent geometry : angle 0.63841 / 0.37 (11576) SS BOND : bond 0.00891 / 0.45 ( 6) SS BOND : angle 1.67849 / 1.21 ( 12) hydrogen bonds : bond 0.17982 / 12.20 ( 416) hydrogen bonds : angle 6.76007 / 4.89 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.5967 (tm) REVERT: A 222 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7233 (ppt170) REVERT: A 285 MET cc_start: 0.6129 (ttp) cc_final: 0.5163 (tpt) REVERT: C 175 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: C 314 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7380 (ttp-110) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.4036 time to fit residues: 57.3154 Evaluate side-chains 112 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS C 259 GLN C 295 ASN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.234672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162380 restraints weight = 8525.983| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.02 r_work: 0.3604 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8560 Z= 0.153 Angle : 0.600 8.078 11588 Z= 0.319 Chirality : 0.043 0.137 1308 Planarity : 0.005 0.068 1460 Dihedral : 5.722 49.778 1174 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.06 % Allowed : 18.11 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1048 helix: 1.90 (0.28), residues: 343 sheet: 0.68 (0.29), residues: 296 loop : -0.25 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.016 0.002 TYR E 190 PHE 0.017 0.002 PHE A 74 TRP 0.016 0.002 TRP C 339 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8554) covalent geometry : angle 0.59631 / 0.32 (11576) SS BOND : bond 0.01168 / 0.60 ( 6) SS BOND : angle 2.10710 / 1.50 ( 12) hydrogen bonds : bond 0.04374 / 2.88 ( 416) hydrogen bonds : angle 4.98224 / 3.53 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6668 (mp) cc_final: 0.6189 (tt) REVERT: A 76 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6298 (tp) REVERT: A 167 MET cc_start: 0.3329 (tpp) cc_final: 0.3037 (tpp) REVERT: A 222 ARG cc_start: 0.7695 (ptp-170) cc_final: 0.7280 (ptt90) REVERT: A 285 MET cc_start: 0.6063 (ttp) cc_final: 0.5123 (tpt) REVERT: B 198 MET cc_start: 0.7937 (mmm) cc_final: 0.7499 (mmm) REVERT: B 345 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6753 (mptt) REVERT: C 61 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8542 (ppp) REVERT: E 39 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: E 43 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7156 (tmmt) outliers start: 37 outliers final: 12 residues processed: 142 average time/residue: 0.3936 time to fit residues: 59.9715 Evaluate side-chains 117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.0070 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS B 195 HIS C 156 GLN C 259 GLN E 39 GLN E 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.230653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156618 restraints weight = 8399.020| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.21 r_work: 0.3561 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8560 Z= 0.259 Angle : 0.718 11.738 11588 Z= 0.375 Chirality : 0.047 0.172 1308 Planarity : 0.005 0.062 1460 Dihedral : 5.326 31.615 1156 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.94 % Allowed : 19.10 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1048 helix: 1.94 (0.28), residues: 332 sheet: 0.51 (0.29), residues: 285 loop : -0.42 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 253 TYR 0.020 0.003 TYR C 59 PHE 0.021 0.002 PHE A 197 TRP 0.020 0.002 TRP E 47 HIS 0.008 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 ( 8554) covalent geometry : angle 0.71121 / 0.37 (11576) SS BOND : bond 0.01729 / 0.88 ( 6) SS BOND : angle 3.06238 / 2.20 ( 12) hydrogen bonds : bond 0.04681 / 3.10 ( 416) hydrogen bonds : angle 5.09360 / 3.62 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6651 (mp) cc_final: 0.6173 (tt) REVERT: A 76 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6535 (tp) REVERT: A 89 ARG cc_start: 0.6955 (mtt180) cc_final: 0.5938 (ptt180) REVERT: A 150 LEU cc_start: 0.6859 (tp) cc_final: 0.6627 (tt) REVERT: A 167 MET cc_start: 0.3369 (tpp) cc_final: 0.3025 (tpp) REVERT: A 227 LYS cc_start: 0.6559 (ttpt) cc_final: 0.6181 (pptt) REVERT: A 228 ARG cc_start: 0.6453 (ttm-80) cc_final: 0.5732 (ptt90) REVERT: A 285 MET cc_start: 0.6201 (ttp) cc_final: 0.5245 (tpt) REVERT: B 345 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7225 (mptt) REVERT: C 43 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.6986 (mt) REVERT: C 175 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7746 (mm-40) REVERT: E 39 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: E 43 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6453 (ttpt) REVERT: E 244 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8076 (ttpp) outliers start: 45 outliers final: 20 residues processed: 147 average time/residue: 0.4875 time to fit residues: 76.4157 Evaluate side-chains 139 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 195 HIS C 259 GLN C 295 ASN E 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.233798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159178 restraints weight = 8587.368| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.97 r_work: 0.3606 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8560 Z= 0.129 Angle : 0.586 9.457 11588 Z= 0.305 Chirality : 0.042 0.168 1308 Planarity : 0.004 0.054 1460 Dihedral : 4.782 33.112 1156 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.95 % Allowed : 22.83 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 1048 helix: 2.19 (0.28), residues: 338 sheet: 0.55 (0.30), residues: 288 loop : -0.24 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 253 TYR 0.016 0.001 TYR E 190 PHE 0.019 0.002 PHE A 197 TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8554) covalent geometry : angle 0.58234 / 0.30 (11576) SS BOND : bond 0.01057 / 0.54 ( 6) SS BOND : angle 1.97987 / 1.44 ( 12) hydrogen bonds : bond 0.03891 / 2.55 ( 416) hydrogen bonds : angle 4.71105 / 3.33 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6646 (mp) cc_final: 0.6236 (tt) REVERT: A 60 LYS cc_start: 0.5826 (OUTLIER) cc_final: 0.5478 (tppt) REVERT: A 95 PHE cc_start: 0.4654 (m-80) cc_final: 0.4454 (m-80) REVERT: A 150 LEU cc_start: 0.6860 (tp) cc_final: 0.6641 (tt) REVERT: A 225 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5544 (mmpt) REVERT: A 227 LYS cc_start: 0.6469 (ttpt) cc_final: 0.6128 (pptt) REVERT: A 228 ARG cc_start: 0.6292 (ttm-80) cc_final: 0.5714 (ptt180) REVERT: A 285 MET cc_start: 0.6244 (ttp) cc_final: 0.5323 (tpt) REVERT: B 198 MET cc_start: 0.7961 (mmm) cc_final: 0.7447 (mmm) REVERT: E 39 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: E 43 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6544 (ttpt) REVERT: E 244 LYS cc_start: 0.8648 (tppp) cc_final: 0.8268 (tppt) outliers start: 36 outliers final: 15 residues processed: 133 average time/residue: 0.4704 time to fit residues: 67.1328 Evaluate side-chains 123 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 0.0270 chunk 33 optimal weight: 20.0000 overall best weight: 1.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.231001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.157699 restraints weight = 8513.267| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.14 r_work: 0.3579 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8560 Z= 0.221 Angle : 0.683 10.570 11588 Z= 0.353 Chirality : 0.046 0.159 1308 Planarity : 0.005 0.054 1460 Dihedral : 4.939 22.215 1151 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.38 % Allowed : 22.28 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1048 helix: 2.19 (0.28), residues: 331 sheet: 0.47 (0.29), residues: 288 loop : -0.31 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 TYR 0.018 0.002 TYR E 103 PHE 0.025 0.002 PHE B 354 TRP 0.019 0.002 TRP E 47 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 ( 8554) covalent geometry : angle 0.67793 / 0.35 (11576) SS BOND : bond 0.01599 / 0.81 ( 6) SS BOND : angle 2.70376 / 1.98 ( 12) hydrogen bonds : bond 0.04302 / 2.86 ( 416) hydrogen bonds : angle 4.92912 / 3.50 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6690 (mp) cc_final: 0.6191 (tt) REVERT: A 74 PHE cc_start: 0.6104 (t80) cc_final: 0.5901 (t80) REVERT: A 76 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6739 (tp) REVERT: A 216 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6165 (mtp85) REVERT: A 222 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.6662 (mmt90) REVERT: A 225 LYS cc_start: 0.5889 (OUTLIER) cc_final: 0.5153 (mmpt) REVERT: A 227 LYS cc_start: 0.6581 (ttpt) cc_final: 0.6096 (pptt) REVERT: A 228 ARG cc_start: 0.6331 (ttm-80) cc_final: 0.5599 (ptt180) REVERT: A 285 MET cc_start: 0.6341 (ttp) cc_final: 0.5390 (tpt) REVERT: B 198 MET cc_start: 0.8038 (mmm) cc_final: 0.7511 (mmm) REVERT: C 43 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6877 (mt) REVERT: C 175 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7709 (mm-40) REVERT: C 314 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7876 (ttp-110) REVERT: E 39 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: E 43 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6602 (ttpt) REVERT: E 244 LYS cc_start: 0.8594 (tppp) cc_final: 0.8213 (tppt) outliers start: 49 outliers final: 29 residues processed: 145 average time/residue: 0.4336 time to fit residues: 67.5862 Evaluate side-chains 147 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.232452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157910 restraints weight = 8435.102| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.88 r_work: 0.3597 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8560 Z= 0.170 Angle : 0.640 9.682 11588 Z= 0.329 Chirality : 0.044 0.182 1308 Planarity : 0.004 0.051 1460 Dihedral : 4.715 21.559 1151 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.94 % Allowed : 23.38 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1048 helix: 2.13 (0.28), residues: 337 sheet: 0.52 (0.30), residues: 280 loop : -0.23 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 TYR 0.017 0.002 TYR A 87 PHE 0.017 0.002 PHE A 197 TRP 0.017 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 8554) covalent geometry : angle 0.63508 / 0.33 (11576) SS BOND : bond 0.01370 / 0.69 ( 6) SS BOND : angle 2.49320 / 1.79 ( 12) hydrogen bonds : bond 0.03999 / 2.64 ( 416) hydrogen bonds : angle 4.81075 / 3.40 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6644 (mp) cc_final: 0.6196 (tt) REVERT: A 74 PHE cc_start: 0.6042 (t80) cc_final: 0.5825 (t80) REVERT: A 150 LEU cc_start: 0.7024 (tp) cc_final: 0.6805 (tt) REVERT: A 166 LYS cc_start: 0.6143 (mmmt) cc_final: 0.5598 (mptt) REVERT: A 222 ARG cc_start: 0.8025 (ptp-170) cc_final: 0.6821 (mmt90) REVERT: A 225 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5177 (mmpt) REVERT: A 227 LYS cc_start: 0.6590 (ttpt) cc_final: 0.6110 (pptt) REVERT: A 228 ARG cc_start: 0.6466 (ttm-80) cc_final: 0.5756 (ptt180) REVERT: A 285 MET cc_start: 0.6337 (ttp) cc_final: 0.5428 (tpt) REVERT: B 198 MET cc_start: 0.8064 (mmm) cc_final: 0.7820 (mmm) REVERT: C 314 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7881 (ttp-110) REVERT: E 39 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: E 43 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6817 (ttpm) REVERT: E 244 LYS cc_start: 0.8736 (tppp) cc_final: 0.8346 (tppt) outliers start: 45 outliers final: 27 residues processed: 143 average time/residue: 0.4809 time to fit residues: 73.7856 Evaluate side-chains 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.231684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157345 restraints weight = 8491.476| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.95 r_work: 0.3576 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8560 Z= 0.185 Angle : 0.654 10.033 11588 Z= 0.337 Chirality : 0.044 0.172 1308 Planarity : 0.005 0.050 1460 Dihedral : 4.774 22.355 1151 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.38 % Allowed : 23.71 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1048 helix: 2.12 (0.28), residues: 337 sheet: 0.47 (0.30), residues: 280 loop : -0.22 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.017 0.002 TYR A 87 PHE 0.020 0.002 PHE A 21 TRP 0.018 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 8554) covalent geometry : angle 0.64929 / 0.33 (11576) SS BOND : bond 0.01454 / 0.74 ( 6) SS BOND : angle 2.63825 / 1.92 ( 12) hydrogen bonds : bond 0.04094 / 2.70 ( 416) hydrogen bonds : angle 4.84875 / 3.44 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6629 (mp) cc_final: 0.6217 (tt) REVERT: A 136 LEU cc_start: 0.6862 (tp) cc_final: 0.6651 (tt) REVERT: A 150 LEU cc_start: 0.6883 (tp) cc_final: 0.6650 (tt) REVERT: A 167 MET cc_start: 0.2745 (tpp) cc_final: 0.2531 (tpp) REVERT: A 216 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6227 (mtp85) REVERT: A 222 ARG cc_start: 0.8057 (ptp-170) cc_final: 0.6826 (mmt90) REVERT: A 225 LYS cc_start: 0.5761 (OUTLIER) cc_final: 0.5162 (mmpt) REVERT: A 228 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6095 (ttt-90) REVERT: A 285 MET cc_start: 0.6345 (ttp) cc_final: 0.5373 (tpt) REVERT: B 198 MET cc_start: 0.8048 (mmm) cc_final: 0.7633 (mmm) REVERT: B 345 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6949 (mtpt) REVERT: C 43 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7033 (mt) REVERT: C 175 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7861 (mm-40) REVERT: C 314 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7866 (ttp-110) REVERT: E 39 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: E 43 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6845 (ttpm) REVERT: E 244 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8358 (tppt) outliers start: 49 outliers final: 27 residues processed: 142 average time/residue: 0.4871 time to fit residues: 74.1965 Evaluate side-chains 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS B 213 HIS C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.231540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161497 restraints weight = 8417.780| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.06 r_work: 0.3595 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8560 Z= 0.199 Angle : 0.670 11.018 11588 Z= 0.345 Chirality : 0.045 0.183 1308 Planarity : 0.005 0.051 1460 Dihedral : 4.831 24.599 1151 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.38 % Allowed : 23.82 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.27), residues: 1048 helix: 2.12 (0.28), residues: 337 sheet: 0.43 (0.30), residues: 280 loop : -0.22 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.017 0.002 TYR A 87 PHE 0.036 0.002 PHE A 74 TRP 0.018 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 8554) covalent geometry : angle 0.66345 / 0.34 (11576) SS BOND : bond 0.01616 / 0.82 ( 6) SS BOND : angle 3.02383 / 2.18 ( 12) hydrogen bonds : bond 0.04145 / 2.75 ( 416) hydrogen bonds : angle 4.87686 / 3.46 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6625 (mp) cc_final: 0.6216 (tt) REVERT: A 63 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7229 (mpt-90) REVERT: A 106 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.4546 (ttp) REVERT: A 136 LEU cc_start: 0.7047 (tp) cc_final: 0.6829 (tt) REVERT: A 150 LEU cc_start: 0.6876 (tp) cc_final: 0.6642 (tt) REVERT: A 216 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6203 (mtp85) REVERT: A 222 ARG cc_start: 0.8045 (ptp-170) cc_final: 0.6851 (mmt90) REVERT: A 225 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5156 (mmpt) REVERT: A 228 ARG cc_start: 0.6458 (ttm-80) cc_final: 0.5996 (ttt-90) REVERT: A 285 MET cc_start: 0.6364 (ttp) cc_final: 0.5385 (tpt) REVERT: B 198 MET cc_start: 0.8041 (mmm) cc_final: 0.7665 (mmm) REVERT: B 213 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.4008 (p90) REVERT: B 345 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6979 (mtpt) REVERT: C 43 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7002 (mt) REVERT: C 314 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7774 (ttp-110) REVERT: D 58 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: E 39 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: E 43 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6795 (ttpm) REVERT: E 244 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8333 (tppt) outliers start: 49 outliers final: 30 residues processed: 140 average time/residue: 0.5189 time to fit residues: 77.7139 Evaluate side-chains 149 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS B 213 HIS C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.232641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161236 restraints weight = 8433.821| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.01 r_work: 0.3602 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8560 Z= 0.157 Angle : 0.635 9.506 11588 Z= 0.326 Chirality : 0.043 0.197 1308 Planarity : 0.004 0.049 1460 Dihedral : 4.689 24.846 1151 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.50 % Allowed : 24.70 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.27), residues: 1048 helix: 2.22 (0.28), residues: 337 sheet: 0.42 (0.30), residues: 280 loop : -0.17 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.020 0.002 TYR A 87 PHE 0.016 0.002 PHE A 197 TRP 0.016 0.002 TRP E 47 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8554) covalent geometry : angle 0.63004 / 0.32 (11576) SS BOND : bond 0.01328 / 0.67 ( 6) SS BOND : angle 2.55758 / 1.83 ( 12) hydrogen bonds : bond 0.03904 / 2.57 ( 416) hydrogen bonds : angle 4.76145 / 3.37 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6598 (mp) cc_final: 0.6202 (tt) REVERT: A 63 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7210 (mpt-90) REVERT: A 106 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.4584 (ttp) REVERT: A 150 LEU cc_start: 0.6828 (tp) cc_final: 0.6601 (tt) REVERT: A 216 ARG cc_start: 0.6485 (mtp85) cc_final: 0.6211 (mtp85) REVERT: A 222 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.6935 (mmt90) REVERT: A 225 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5191 (mmpt) REVERT: A 228 ARG cc_start: 0.6583 (ttm-80) cc_final: 0.6035 (ttt-90) REVERT: A 285 MET cc_start: 0.6341 (ttp) cc_final: 0.5364 (tpt) REVERT: B 198 MET cc_start: 0.8049 (mmm) cc_final: 0.7667 (mmm) REVERT: B 213 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.6257 (p-80) REVERT: C 43 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7089 (mt) REVERT: C 314 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7807 (ttp-110) REVERT: D 58 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: E 39 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: E 244 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8281 (tppt) outliers start: 41 outliers final: 25 residues processed: 138 average time/residue: 0.5256 time to fit residues: 77.8800 Evaluate side-chains 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS B 213 HIS C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.233114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157983 restraints weight = 8443.695| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.90 r_work: 0.3610 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8560 Z= 0.145 Angle : 0.635 9.208 11588 Z= 0.323 Chirality : 0.043 0.204 1308 Planarity : 0.004 0.049 1460 Dihedral : 4.629 24.729 1151 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.95 % Allowed : 25.58 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1048 helix: 2.14 (0.28), residues: 343 sheet: 0.40 (0.30), residues: 280 loop : -0.22 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.021 0.002 TYR A 87 PHE 0.041 0.002 PHE A 74 TRP 0.016 0.002 TRP E 47 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8554) covalent geometry : angle 0.63049 / 0.32 (11576) SS BOND : bond 0.01233 / 0.63 ( 6) SS BOND : angle 2.38671 / 1.71 ( 12) hydrogen bonds : bond 0.03837 / 2.54 ( 416) hydrogen bonds : angle 4.71009 / 3.34 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6591 (mp) cc_final: 0.6202 (tt) REVERT: A 63 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7145 (mpt-90) REVERT: A 106 MET cc_start: 0.5561 (OUTLIER) cc_final: 0.4640 (ttp) REVERT: A 136 LEU cc_start: 0.7327 (tt) cc_final: 0.7048 (pp) REVERT: A 150 LEU cc_start: 0.6806 (tp) cc_final: 0.6591 (tt) REVERT: A 216 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.6248 (mtp85) REVERT: A 222 ARG cc_start: 0.7942 (ptp-170) cc_final: 0.7390 (mtm180) REVERT: A 225 LYS cc_start: 0.5728 (OUTLIER) cc_final: 0.5054 (mmpt) REVERT: A 228 ARG cc_start: 0.6565 (ttm-80) cc_final: 0.5956 (ptt180) REVERT: A 285 MET cc_start: 0.6307 (ttp) cc_final: 0.5136 (tpt) REVERT: A 288 MET cc_start: 0.7278 (ttp) cc_final: 0.6213 (ppp) REVERT: B 198 MET cc_start: 0.8014 (mmm) cc_final: 0.7647 (mmm) REVERT: C 43 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7053 (mt) REVERT: C 314 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7734 (ttp-110) REVERT: D 58 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: E 39 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: E 98 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7977 (ttp-170) REVERT: E 244 LYS cc_start: 0.8646 (tppp) cc_final: 0.8258 (tppt) outliers start: 36 outliers final: 24 residues processed: 130 average time/residue: 0.5604 time to fit residues: 77.8373 Evaluate side-chains 138 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 4 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 195 HIS B 213 HIS C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.232272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166540 restraints weight = 8451.582| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.98 r_work: 0.3650 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8560 Z= 0.174 Angle : 0.667 12.415 11588 Z= 0.338 Chirality : 0.044 0.206 1308 Planarity : 0.004 0.050 1460 Dihedral : 4.726 26.268 1151 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.95 % Allowed : 25.36 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1048 helix: 2.21 (0.28), residues: 336 sheet: 0.37 (0.30), residues: 280 loop : -0.23 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.022 0.002 TYR A 87 PHE 0.016 0.002 PHE A 197 TRP 0.018 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 8554) covalent geometry : angle 0.66232 / 0.34 (11576) SS BOND : bond 0.01438 / 0.73 ( 6) SS BOND : angle 2.65854 / 1.91 ( 12) hydrogen bonds : bond 0.03992 / 2.64 ( 416) hydrogen bonds : angle 4.77313 / 3.39 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.06 seconds wall clock time: 60 minutes 29.80 seconds (3629.80 seconds total)