Starting phenix.real_space_refine on Thu Jul 2 05:23:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pkm_17747/07_2026/8pkm_17747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pkm_17747/07_2026/8pkm_17747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pkm_17747/07_2026/8pkm_17747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pkm_17747/07_2026/8pkm_17747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pkm_17747/07_2026/8pkm_17747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pkm_17747/07_2026/8pkm_17747.map" } resolution = 2.9 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= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 Cl 1 4.86 5 C 4416 2.51 5 N 1173 2.21 5 O 1281 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6929 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1734 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2539 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2174 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 2 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'CLR': 1, 'T7M': 1, 'ZKV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'T7M:plan-3': 1, 'T7M:plan-4': 1, 'T7M:plan-5': 1, 'T7M:plan-6': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 1.73, per 1000 atoms: 0.25 Number of scatterers: 6929 At special positions: 0 Unit cell: (74.9275, 98.685, 125.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 54 16.00 P 2 15.00 F 2 9.00 O 1281 8.00 N 1173 7.00 C 4416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 0.66 Conformation dependent library (CDL) restraints added in 434.8 milliseconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 9 sheets defined 47.5% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.738A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.556A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.229A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.939A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.713A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.714A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.954A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.823A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 46 removed outlier: 4.594A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 63 removed outlier: 3.711A pdb=" N THR R 39 " --> pdb=" O TYR R 35 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER R 40 " --> pdb=" O GLN R 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 43 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 99 removed outlier: 4.471A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 106 through 140 removed outlier: 3.880A pdb=" N THR R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'R' and resid 149 through 174 removed outlier: 3.886A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 229 Processing helix chain 'R' and resid 329 through 368 removed outlier: 3.634A pdb=" N CYS R 357 " --> pdb=" O THR R 353 " (cutoff:3.500A) Proline residue: R 360 - end of helix removed outlier: 3.570A pdb=" N VAL R 364 " --> pdb=" O PRO R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.935A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.321A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.002A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.534A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.753A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.892A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.918A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.606A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.536A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.668A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1059 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: 1.09 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1202 1.32 - 1.45: 1815 1.45 - 1.57: 3968 1.57 - 1.69: 3 1.69 - 1.81: 77 Bond restraints: 7065 Sorted by residual: bond pdb=" O4 T7M R 502 " pdb=" P4 T7M R 502 " ideal model delta sigma weight residual 1.704 1.624 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O13 T7M R 502 " pdb=" P1 T7M R 502 " ideal model delta sigma weight residual 1.659 1.596 0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" C07 ZKV R 503 " pdb=" N02 ZKV R 503 " ideal model delta sigma weight residual 1.445 1.498 -0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" C08 ZKV R 503 " pdb=" N02 ZKV R 503 " ideal model delta sigma weight residual 1.446 1.492 -0.046 2.00e-02 2.50e+03 5.24e+00 bond pdb=" C4 T7M R 502 " pdb=" O4 T7M R 502 " ideal model delta sigma weight residual 1.402 1.443 -0.041 2.00e-02 2.50e+03 4.15e+00 ... (remaining 7060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 9390 1.54 - 3.08: 149 3.08 - 4.62: 24 4.62 - 6.15: 12 6.15 - 7.69: 2 Bond angle restraints: 9577 Sorted by residual: angle pdb=" N ILE R 169 " pdb=" CA ILE R 169 " pdb=" C ILE R 169 " ideal model delta sigma weight residual 108.88 115.24 -6.36 2.16e+00 2.14e-01 8.67e+00 angle pdb=" CA LEU R 52 " pdb=" CB LEU R 52 " pdb=" CG LEU R 52 " ideal model delta sigma weight residual 116.30 123.99 -7.69 3.50e+00 8.16e-02 4.83e+00 angle pdb=" CA ILE R 169 " pdb=" C ILE R 169 " pdb=" N PRO R 170 " ideal model delta sigma weight residual 118.88 122.10 -3.22 1.54e+00 4.22e-01 4.38e+00 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 113.19 -2.49 1.22e+00 6.72e-01 4.18e+00 angle pdb=" C7 T7M R 502 " pdb=" C8 T7M R 502 " pdb=" O16 T7M R 502 " ideal model delta sigma weight residual 113.80 107.70 6.10 3.00e+00 1.11e-01 4.13e+00 ... (remaining 9572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 4257 35.38 - 70.75: 39 70.75 - 106.13: 1 106.13 - 141.50: 3 141.50 - 176.88: 3 Dihedral angle restraints: 4303 sinusoidal: 1760 harmonic: 2543 Sorted by residual: dihedral pdb=" C10 T7M R 502 " pdb=" C8 T7M R 502 " pdb=" O16 T7M R 502 " pdb=" C9 T7M R 502 " ideal model delta sinusoidal sigma weight residual 288.02 111.14 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C10 T7M R 502 " pdb=" C8 T7M R 502 " pdb=" O16 T7M R 502 " pdb=" C7 T7M R 502 " ideal model delta sinusoidal sigma weight residual 55.77 -128.42 -175.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C8 T7M R 502 " pdb=" C7 T7M R 502 " pdb=" O13 T7M R 502 " pdb=" P1 T7M R 502 " ideal model delta sinusoidal sigma weight residual 257.75 95.88 161.87 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 4300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 985 0.067 - 0.133: 116 0.133 - 0.200: 3 0.200 - 0.266: 0 0.266 - 0.333: 1 Chirality restraints: 1105 Sorted by residual: chirality pdb=" C8 T7M R 502 " pdb=" C7 T7M R 502 " pdb=" C9 T7M R 502 " pdb=" O16 T7M R 502 " both_signs ideal model delta sigma weight residual False -2.26 -2.60 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1102 not shown) Planarity restraints: 1194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 ZKV R 503 " 0.027 2.00e-02 2.50e+03 2.24e-02 7.52e+00 pdb=" C12 ZKV R 503 " -0.026 2.00e-02 2.50e+03 pdb=" C14 ZKV R 503 " -0.000 2.00e-02 2.50e+03 pdb=" C15 ZKV R 503 " 0.027 2.00e-02 2.50e+03 pdb=" N03 ZKV R 503 " 0.001 2.00e-02 2.50e+03 pdb=" O01 ZKV R 503 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO R 171 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C14 ZKV R 503 " -0.018 2.00e-02 2.50e+03 9.30e-03 1.95e+00 pdb=" C15 ZKV R 503 " 0.010 2.00e-02 2.50e+03 pdb=" C16 ZKV R 503 " 0.011 2.00e-02 2.50e+03 pdb=" C17 ZKV R 503 " 0.004 2.00e-02 2.50e+03 pdb=" C18 ZKV R 503 " -0.002 2.00e-02 2.50e+03 pdb=" C19 ZKV R 503 " -0.000 2.00e-02 2.50e+03 pdb=" C20 ZKV R 503 " 0.005 2.00e-02 2.50e+03 pdb=" F01 ZKV R 503 " -0.013 2.00e-02 2.50e+03 pdb="CL01 ZKV R 503 " 0.005 2.00e-02 2.50e+03 ... (remaining 1191 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1002 2.76 - 3.29: 6932 3.29 - 3.83: 12170 3.83 - 4.36: 14286 4.36 - 4.90: 24851 Nonbonded interactions: 59241 Sorted by model distance: nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.220 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR R 346 " pdb=" O6 T7M R 502 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.282 3.120 nonbonded pdb=" OG1 THR A 324 " pdb=" OD1 ASN A 331 " model vdw 2.288 3.040 ... (remaining 59236 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: 1.440 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7066 Z= 0.155 Angle : 0.530 7.692 9579 Z= 0.268 Chirality : 0.042 0.333 1105 Planarity : 0.004 0.037 1194 Dihedral : 12.988 176.875 2650 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.94 % Allowed : 7.13 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.29), residues: 858 helix: 1.80 (0.27), residues: 384 sheet: -0.59 (0.37), residues: 182 loop : -0.67 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 339 TYR 0.013 0.001 TYR R 195 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 7065) covalent geometry : angle 0.52989 / 0.27 ( 9577) SS BOND : bond 0.00131 / 0.07 ( 1) SS BOND : angle 0.17679 / 0.10 ( 2) hydrogen bonds : bond 0.07354 / 5.55 ( 365) hydrogen bonds : angle 4.80300 / 3.31 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.7261 (m-40) cc_final: 0.7041 (m110) REVERT: B 226 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6174 (mt-10) REVERT: R 84 MET cc_start: 0.7501 (mtp) cc_final: 0.7283 (mtp) REVERT: R 334 LYS cc_start: 0.6670 (tmtt) cc_final: 0.6357 (tmmt) REVERT: R 335 MET cc_start: 0.6550 (ttm) cc_final: 0.6326 (ttp) REVERT: R 345 LYS cc_start: 0.6997 (tttt) cc_final: 0.6555 (ttmt) outliers start: 7 outliers final: 3 residues processed: 113 average time/residue: 0.5191 time to fit residues: 62.0547 Evaluate side-chains 84 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 ASN R 72 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.215630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.182232 restraints weight = 7236.117| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.76 r_work: 0.4121 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7066 Z= 0.201 Angle : 0.648 8.291 9579 Z= 0.327 Chirality : 0.045 0.163 1105 Planarity : 0.005 0.055 1194 Dihedral : 11.048 165.601 1082 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.63 % Allowed : 11.17 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.29), residues: 858 helix: 1.25 (0.27), residues: 386 sheet: -0.89 (0.35), residues: 191 loop : -0.84 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 49 TYR 0.018 0.002 TYR R 195 PHE 0.018 0.002 PHE A 196 TRP 0.017 0.002 TRP B 99 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 7065) covalent geometry : angle 0.64793 / 0.33 ( 9577) SS BOND : bond 0.00417 / 0.22 ( 1) SS BOND : angle 0.34728 / 0.19 ( 2) hydrogen bonds : bond 0.04350 / 3.00 ( 365) hydrogen bonds : angle 4.88133 / 3.36 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.328 Fit side-chains REVERT: A 33 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 308 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 318 GLU cc_start: 0.6694 (pt0) cc_final: 0.6370 (pt0) REVERT: B 201 SER cc_start: 0.8145 (p) cc_final: 0.7808 (m) REVERT: B 226 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6411 (mt-10) REVERT: B 258 ASP cc_start: 0.6247 (t0) cc_final: 0.6041 (t0) REVERT: G 38 MET cc_start: 0.5576 (mpt) cc_final: 0.5215 (mpt) REVERT: R 38 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.6831 (mt) REVERT: R 334 LYS cc_start: 0.6894 (tmtt) cc_final: 0.6588 (tmmt) REVERT: R 335 MET cc_start: 0.6991 (ttm) cc_final: 0.6774 (ttp) REVERT: R 345 LYS cc_start: 0.7106 (tttt) cc_final: 0.6805 (tttt) outliers start: 27 outliers final: 14 residues processed: 106 average time/residue: 0.4682 time to fit residues: 52.7960 Evaluate side-chains 94 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 241 ASN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.219002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.186134 restraints weight = 7185.373| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 1.75 r_work: 0.4151 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7066 Z= 0.125 Angle : 0.540 7.641 9579 Z= 0.278 Chirality : 0.042 0.147 1105 Planarity : 0.004 0.051 1194 Dihedral : 10.548 158.871 1082 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.77 % Allowed : 13.06 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.29), residues: 858 helix: 1.55 (0.27), residues: 380 sheet: -0.74 (0.36), residues: 184 loop : -0.74 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.015 0.001 TYR R 195 PHE 0.017 0.002 PHE B 292 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7065) covalent geometry : angle 0.54031 / 0.28 ( 9577) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.14767 / 0.08 ( 2) hydrogen bonds : bond 0.03652 / 2.54 ( 365) hydrogen bonds : angle 4.74350 / 3.28 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.248 Fit side-chains REVERT: A 33 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 240 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3992 (tpp) REVERT: A 308 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 201 SER cc_start: 0.8113 (p) cc_final: 0.7754 (m) REVERT: B 226 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6456 (mt-10) REVERT: B 234 PHE cc_start: 0.4647 (OUTLIER) cc_final: 0.4299 (t80) REVERT: G 38 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4856 (mpt) REVERT: R 38 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6823 (mt) REVERT: R 334 LYS cc_start: 0.6857 (tmtt) cc_final: 0.6556 (tmmt) REVERT: R 335 MET cc_start: 0.6918 (ttm) cc_final: 0.6685 (ttp) REVERT: R 345 LYS cc_start: 0.6995 (tttt) cc_final: 0.6703 (tttt) REVERT: R 385 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4720 (mp) outliers start: 28 outliers final: 14 residues processed: 107 average time/residue: 0.4839 time to fit residues: 54.9796 Evaluate side-chains 100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.218774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185906 restraints weight = 7213.210| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.75 r_work: 0.4134 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7066 Z= 0.129 Angle : 0.539 7.440 9579 Z= 0.276 Chirality : 0.042 0.149 1105 Planarity : 0.004 0.052 1194 Dihedral : 10.230 149.072 1082 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.17 % Allowed : 14.00 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.29), residues: 858 helix: 1.61 (0.27), residues: 381 sheet: -0.57 (0.37), residues: 171 loop : -0.81 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.015 0.001 TYR R 195 PHE 0.018 0.002 PHE B 292 TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7065) covalent geometry : angle 0.53880 / 0.28 ( 9577) SS BOND : bond 0.00193 / 0.10 ( 1) SS BOND : angle 0.11555 / 0.06 ( 2) hydrogen bonds : bond 0.03634 / 2.51 ( 365) hydrogen bonds : angle 4.71380 / 3.27 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.5747 (ptt) cc_final: 0.4998 (tmm) REVERT: A 33 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 240 MET cc_start: 0.4493 (OUTLIER) cc_final: 0.4148 (tpp) REVERT: A 308 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: B 201 SER cc_start: 0.8104 (p) cc_final: 0.7745 (m) REVERT: B 226 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6491 (mt-10) REVERT: B 234 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.4274 (t80) REVERT: G 38 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.4851 (mpt) REVERT: R 38 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6816 (mt) REVERT: R 334 LYS cc_start: 0.6873 (tmtt) cc_final: 0.6572 (tmmt) REVERT: R 345 LYS cc_start: 0.7053 (tttt) cc_final: 0.6686 (tttt) REVERT: R 385 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4650 (mp) outliers start: 31 outliers final: 14 residues processed: 108 average time/residue: 0.3991 time to fit residues: 46.3487 Evaluate side-chains 99 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.219490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.186763 restraints weight = 7260.310| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.76 r_work: 0.4156 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7066 Z= 0.124 Angle : 0.544 8.728 9579 Z= 0.275 Chirality : 0.042 0.157 1105 Planarity : 0.004 0.052 1194 Dihedral : 9.955 141.594 1082 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.04 % Allowed : 14.94 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.29), residues: 858 helix: 1.71 (0.27), residues: 379 sheet: -0.59 (0.37), residues: 171 loop : -0.73 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.015 0.001 TYR R 195 PHE 0.017 0.002 PHE B 199 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7065) covalent geometry : angle 0.54397 / 0.27 ( 9577) SS BOND : bond 0.00162 / 0.09 ( 1) SS BOND : angle 0.06332 / 0.03 ( 2) hydrogen bonds : bond 0.03562 / 2.46 ( 365) hydrogen bonds : angle 4.67686 / 3.24 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.264 Fit side-chains REVERT: A 33 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 308 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 201 SER cc_start: 0.8094 (p) cc_final: 0.7711 (m) REVERT: B 226 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6457 (mt-10) REVERT: B 234 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.4270 (t80) REVERT: G 38 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4887 (mpt) REVERT: R 38 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6829 (mt) REVERT: R 334 LYS cc_start: 0.6998 (tmtt) cc_final: 0.6697 (tmmt) REVERT: R 345 LYS cc_start: 0.7010 (tttt) cc_final: 0.6708 (tttt) REVERT: R 385 ILE cc_start: 0.5184 (OUTLIER) cc_final: 0.4649 (mp) outliers start: 30 outliers final: 16 residues processed: 108 average time/residue: 0.4094 time to fit residues: 47.4504 Evaluate side-chains 100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.223488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.191179 restraints weight = 7284.655| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 1.77 r_work: 0.4151 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7066 Z= 0.101 Angle : 0.520 10.317 9579 Z= 0.262 Chirality : 0.041 0.158 1105 Planarity : 0.004 0.051 1194 Dihedral : 9.244 143.885 1082 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.23 % Allowed : 16.42 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.29), residues: 858 helix: 1.91 (0.28), residues: 385 sheet: -0.54 (0.37), residues: 170 loop : -0.67 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.013 0.001 TYR R 195 PHE 0.018 0.001 PHE B 199 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 7065) covalent geometry : angle 0.52006 / 0.26 ( 9577) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 0.19430 / 0.11 ( 2) hydrogen bonds : bond 0.03209 / 2.22 ( 365) hydrogen bonds : angle 4.54659 / 3.14 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.264 Fit side-chains REVERT: A 18 MET cc_start: 0.5672 (ptt) cc_final: 0.4811 (tpt) REVERT: A 33 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 308 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: B 201 SER cc_start: 0.7992 (p) cc_final: 0.7604 (m) REVERT: B 226 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6186 (mt-10) REVERT: B 234 PHE cc_start: 0.4681 (OUTLIER) cc_final: 0.4292 (t80) REVERT: G 38 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4966 (mpt) REVERT: R 38 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.6880 (mt) REVERT: R 334 LYS cc_start: 0.7100 (tmtt) cc_final: 0.6802 (tmmt) REVERT: R 345 LYS cc_start: 0.6950 (tttt) cc_final: 0.6563 (tttt) REVERT: R 385 ILE cc_start: 0.5130 (OUTLIER) cc_final: 0.4592 (mp) outliers start: 24 outliers final: 10 residues processed: 106 average time/residue: 0.4248 time to fit residues: 48.2064 Evaluate side-chains 96 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 0.0570 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 48 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.222228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.189979 restraints weight = 7182.876| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.74 r_work: 0.4140 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7066 Z= 0.114 Angle : 0.527 8.093 9579 Z= 0.269 Chirality : 0.042 0.175 1105 Planarity : 0.004 0.052 1194 Dihedral : 8.826 152.205 1082 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.69 % Allowed : 17.63 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.29), residues: 858 helix: 1.88 (0.27), residues: 385 sheet: -0.37 (0.38), residues: 168 loop : -0.70 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 242 TYR 0.020 0.001 TYR R 144 PHE 0.018 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7065) covalent geometry : angle 0.52680 / 0.27 ( 9577) SS BOND : bond 0.00138 / 0.07 ( 1) SS BOND : angle 0.06760 / 0.04 ( 2) hydrogen bonds : bond 0.03381 / 2.32 ( 365) hydrogen bonds : angle 4.62110 / 3.21 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.256 Fit side-chains REVERT: A 33 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6912 (mt-10) REVERT: B 201 SER cc_start: 0.7993 (p) cc_final: 0.7592 (m) REVERT: B 226 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6184 (mt-10) REVERT: B 234 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.4224 (t80) REVERT: G 38 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4980 (mpt) REVERT: R 38 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.6908 (mt) REVERT: R 334 LYS cc_start: 0.7112 (tmtt) cc_final: 0.6804 (tmmt) REVERT: R 385 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4574 (mp) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 0.4095 time to fit residues: 40.8446 Evaluate side-chains 92 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.219478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186832 restraints weight = 7281.567| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.74 r_work: 0.4111 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7066 Z= 0.137 Angle : 0.556 8.503 9579 Z= 0.282 Chirality : 0.042 0.188 1105 Planarity : 0.004 0.054 1194 Dihedral : 8.188 166.358 1082 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.36 % Allowed : 17.36 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.29), residues: 858 helix: 1.75 (0.27), residues: 385 sheet: -0.56 (0.36), residues: 188 loop : -0.68 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 339 TYR 0.016 0.001 TYR R 195 PHE 0.019 0.002 PHE B 199 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7065) covalent geometry : angle 0.55578 / 0.28 ( 9577) SS BOND : bond 0.00215 / 0.11 ( 1) SS BOND : angle 0.07854 / 0.04 ( 2) hydrogen bonds : bond 0.03662 / 2.51 ( 365) hydrogen bonds : angle 4.68923 / 3.26 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.255 Fit side-chains REVERT: A 33 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 226 GLU cc_start: 0.6505 (mt-10) cc_final: 0.6240 (mt-10) REVERT: B 234 PHE cc_start: 0.4612 (OUTLIER) cc_final: 0.4219 (t80) REVERT: G 38 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4999 (mpt) REVERT: R 38 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.6899 (mt) REVERT: R 334 LYS cc_start: 0.7111 (tmtt) cc_final: 0.6799 (tmmt) REVERT: R 385 ILE cc_start: 0.5136 (OUTLIER) cc_final: 0.4550 (mp) outliers start: 25 outliers final: 17 residues processed: 96 average time/residue: 0.3907 time to fit residues: 40.4234 Evaluate side-chains 95 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.0050 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.221149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.188858 restraints weight = 7233.355| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.74 r_work: 0.4132 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7066 Z= 0.117 Angle : 0.534 8.710 9579 Z= 0.272 Chirality : 0.041 0.163 1105 Planarity : 0.004 0.052 1194 Dihedral : 7.818 172.799 1082 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.10 % Allowed : 18.17 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.29), residues: 858 helix: 1.83 (0.27), residues: 385 sheet: -0.45 (0.36), residues: 182 loop : -0.72 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 148 TYR 0.015 0.001 TYR R 195 PHE 0.018 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7065) covalent geometry : angle 0.53408 / 0.27 ( 9577) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.05048 / 0.03 ( 2) hydrogen bonds : bond 0.03426 / 2.36 ( 365) hydrogen bonds : angle 4.63449 / 3.21 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.247 Fit side-chains REVERT: A 33 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6930 (mt-10) REVERT: B 201 SER cc_start: 0.7986 (p) cc_final: 0.7613 (m) REVERT: B 226 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6196 (mt-10) REVERT: B 234 PHE cc_start: 0.4621 (OUTLIER) cc_final: 0.4214 (t80) REVERT: G 38 MET cc_start: 0.5340 (OUTLIER) cc_final: 0.4992 (mpt) REVERT: R 38 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.6891 (mt) REVERT: R 334 LYS cc_start: 0.7108 (tmtt) cc_final: 0.6802 (tmmt) REVERT: R 385 ILE cc_start: 0.5108 (OUTLIER) cc_final: 0.4524 (mp) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.4463 time to fit residues: 45.7650 Evaluate side-chains 96 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.222759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.189261 restraints weight = 7201.669| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 1.85 r_work: 0.4141 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7066 Z= 0.127 Angle : 0.546 8.858 9579 Z= 0.278 Chirality : 0.042 0.171 1105 Planarity : 0.004 0.052 1194 Dihedral : 7.944 177.450 1082 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.96 % Allowed : 17.77 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.29), residues: 858 helix: 1.77 (0.27), residues: 386 sheet: -0.58 (0.36), residues: 184 loop : -0.75 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 148 TYR 0.015 0.001 TYR R 195 PHE 0.024 0.002 PHE B 292 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7065) covalent geometry : angle 0.54601 / 0.28 ( 9577) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.04435 / 0.02 ( 2) hydrogen bonds : bond 0.03533 / 2.42 ( 365) hydrogen bonds : angle 4.67952 / 3.25 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.242 Fit side-chains REVERT: A 33 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6988 (mt-10) REVERT: B 201 SER cc_start: 0.8019 (p) cc_final: 0.7640 (m) REVERT: B 226 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6150 (mt-10) REVERT: B 234 PHE cc_start: 0.4608 (OUTLIER) cc_final: 0.4183 (t80) REVERT: G 38 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.5134 (mpt) REVERT: R 38 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.6903 (mt) REVERT: R 334 LYS cc_start: 0.7106 (tmtt) cc_final: 0.6796 (tmmt) REVERT: R 385 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4569 (mp) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.3892 time to fit residues: 39.1559 Evaluate side-chains 93 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 0.0870 chunk 40 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.225340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.192112 restraints weight = 7273.893| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.86 r_work: 0.4169 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7066 Z= 0.108 Angle : 0.522 8.842 9579 Z= 0.268 Chirality : 0.041 0.148 1105 Planarity : 0.004 0.052 1194 Dihedral : 7.883 179.157 1082 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.83 % Allowed : 17.90 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.29), residues: 858 helix: 1.93 (0.27), residues: 385 sheet: -0.52 (0.37), residues: 176 loop : -0.69 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 148 TYR 0.015 0.001 TYR R 144 PHE 0.019 0.001 PHE B 292 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7065) covalent geometry : angle 0.52204 / 0.27 ( 9577) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.09204 / 0.05 ( 2) hydrogen bonds : bond 0.03296 / 2.27 ( 365) hydrogen bonds : angle 4.59163 / 3.18 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.09 seconds wall clock time: 41 minutes 7.51 seconds (2467.51 seconds total)