Starting phenix.real_space_refine on Sat Aug 23 02:10:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3q_41008/08_2025/8t3q_41008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3q_41008/08_2025/8t3q_41008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3q_41008/08_2025/8t3q_41008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3q_41008/08_2025/8t3q_41008.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3q_41008/08_2025/8t3q_41008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3q_41008/08_2025/8t3q_41008.cif" } resolution = 3.14 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= 0.034 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 55 5.16 5 C 5752 2.51 5 N 1562 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1800 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2372 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.28 Number of scatterers: 9035 At special positions: 0 Unit cell: (85.284, 124.2, 125.856, 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 55 16.00 O 1666 8.00 N 1562 7.00 C 5752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 328.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.232A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.724A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.759A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.953A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.106A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.949A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.532A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.751A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 35 through 71 removed outlier: 3.568A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 89 Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.653A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.539A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR R 119 " --> pdb=" O PHE R 115 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER R 123 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 200 through 216 Processing helix chain 'R' and resid 216 through 245 removed outlier: 3.675A pdb=" N GLY R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 258 through 291 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 299 through 322 removed outlier: 3.824A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.773A pdb=" N VAL A 109 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.312A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.860A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.924A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.228A 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: 3.973A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.023A 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: 3.920A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.302A 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: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 4.952A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.788A pdb=" N VAL N 148 " --> pdb=" O LYS N 245 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 247 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 180 through 181 445 hydrogen bonds defined for protein. 1254 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: 1.60 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1476 1.32 - 1.44: 2522 1.44 - 1.57: 5141 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 9218 Sorted by residual: bond pdb=" C HIS R 112 " pdb=" O HIS R 112 " ideal model delta sigma weight residual 1.236 1.313 -0.076 1.15e-02 7.56e+03 4.42e+01 bond pdb=" N VAL R 124 " pdb=" CA VAL R 124 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.08e-02 8.57e+03 1.35e+01 bond pdb=" N VAL R 117 " pdb=" CA VAL R 117 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" C PRO R 108 " pdb=" O PRO R 108 " ideal model delta sigma weight residual 1.237 1.195 0.043 1.26e-02 6.30e+03 1.14e+01 ... (remaining 9213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 11667 2.34 - 4.68: 780 4.68 - 7.02: 44 7.02 - 9.35: 9 9.35 - 11.69: 2 Bond angle restraints: 12502 Sorted by residual: angle pdb=" N PRO N 237 " pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 110.95 99.26 11.69 1.62e+00 3.81e-01 5.21e+01 angle pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" C LEU R 120 " ideal model delta sigma weight residual 113.12 105.33 7.79 1.25e+00 6.40e-01 3.88e+01 angle pdb=" N GLN R 290 " pdb=" CA GLN R 290 " pdb=" C GLN R 290 " ideal model delta sigma weight residual 112.23 104.42 7.81 1.26e+00 6.30e-01 3.84e+01 angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 113.42 106.79 6.63 1.17e+00 7.31e-01 3.21e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 109.80 100.71 9.09 1.64e+00 3.72e-01 3.07e+01 ... (remaining 12497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4884 17.15 - 34.31: 438 34.31 - 51.46: 125 51.46 - 68.62: 23 68.62 - 85.77: 7 Dihedral angle restraints: 5477 sinusoidal: 2119 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 157.25 -64.25 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" C TYR N 236 " pdb=" N TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual -122.60 -136.52 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual 122.80 135.12 -12.32 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1197 0.100 - 0.200: 214 0.200 - 0.300: 25 0.300 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA TYR N 236 " pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CB TYR N 236 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1435 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 401 " 0.098 2.00e-02 2.50e+03 2.26e-01 5.11e+02 pdb=" C4 HXA R 401 " -0.301 2.00e-02 2.50e+03 pdb=" C5 HXA R 401 " 0.306 2.00e-02 2.50e+03 pdb=" C6 HXA R 401 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 401 " -0.069 2.00e-02 2.50e+03 1.33e-01 1.77e+02 pdb=" C7 HXA R 401 " 0.175 2.00e-02 2.50e+03 pdb=" C8 HXA R 401 " -0.175 2.00e-02 2.50e+03 pdb=" C9 HXA R 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 HXA R 401 " 0.102 2.00e-02 2.50e+03 1.02e-01 1.04e+02 pdb=" C19 HXA R 401 " -0.101 2.00e-02 2.50e+03 pdb=" C20 HXA R 401 " -0.103 2.00e-02 2.50e+03 pdb=" C21 HXA R 401 " 0.102 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 323 2.69 - 3.25: 8908 3.25 - 3.80: 14332 3.80 - 4.35: 19120 4.35 - 4.90: 31430 Nonbonded interactions: 74113 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR N 176 " model vdw 2.144 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.144 3.040 nonbonded pdb=" OG SER N 157 " pdb=" OG1 THR N 214 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.292 3.040 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.297 3.120 ... (remaining 74108 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 9221 Z= 0.573 Angle : 1.152 11.693 12508 Z= 0.813 Chirality : 0.074 0.501 1438 Planarity : 0.009 0.226 1589 Dihedral : 14.658 85.772 3294 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.75 % Allowed : 16.63 % Favored : 81.62 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.14 (0.25), residues: 1141 helix: -0.17 (0.27), residues: 375 sheet: -0.39 (0.32), residues: 270 loop : -1.33 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 194 TYR 0.032 0.002 TYR N 236 PHE 0.021 0.002 PHE B 151 TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00793 ( 9218) covalent geometry : angle 1.15104 (12502) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.93044 ( 6) hydrogen bonds : bond 0.20773 ( 445) hydrogen bonds : angle 7.48234 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6652 (m-40) cc_final: 0.6419 (m-40) REVERT: B 197 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6391 (mmt180) REVERT: B 214 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7266 (ttp80) REVERT: B 217 MET cc_start: 0.6285 (mtt) cc_final: 0.5734 (ptp) REVERT: B 219 ARG cc_start: 0.6923 (mtt-85) cc_final: 0.6637 (mtp85) REVERT: N 235 GLU cc_start: 0.6954 (pt0) cc_final: 0.6604 (mt-10) REVERT: R 22 ARG cc_start: 0.4006 (mmp-170) cc_final: 0.2996 (mpp-170) REVERT: R 24 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6574 (mtp180) REVERT: R 106 LEU cc_start: 0.8623 (mt) cc_final: 0.8415 (mt) REVERT: R 118 MET cc_start: 0.6056 (ttp) cc_final: 0.5672 (mtp) REVERT: R 215 ASN cc_start: 0.8202 (m-40) cc_final: 0.7360 (m-40) outliers start: 17 outliers final: 5 residues processed: 159 average time/residue: 0.1249 time to fit residues: 26.3538 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 244 ASN B 9 GLN B 44 GLN B 88 ASN R 112 HIS R 142 HIS R 182 GLN R 258 GLN R 290 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119692 restraints weight = 10195.930| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.80 r_work: 0.3203 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9221 Z= 0.221 Angle : 0.667 9.448 12508 Z= 0.353 Chirality : 0.045 0.211 1438 Planarity : 0.005 0.077 1589 Dihedral : 6.309 53.808 1280 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.39 % Allowed : 16.43 % Favored : 80.18 % 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 aren not related in a simple way. whole: -0.73 (0.25), residues: 1141 helix: 0.41 (0.26), residues: 379 sheet: -0.42 (0.33), residues: 259 loop : -1.14 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.019 0.002 TYR N 236 PHE 0.022 0.002 PHE R 27 TRP 0.022 0.002 TRP B 211 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9218) covalent geometry : angle 0.66664 (12502) SS BOND : bond 0.00387 ( 3) SS BOND : angle 1.54275 ( 6) hydrogen bonds : bond 0.05142 ( 445) hydrogen bonds : angle 5.10984 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.7334 (tttp) cc_final: 0.6784 (ttmm) REVERT: A 145 LYS cc_start: 0.7511 (mttp) cc_final: 0.7250 (mttp) REVERT: A 199 ASP cc_start: 0.6830 (m-30) cc_final: 0.6594 (m-30) REVERT: A 238 MET cc_start: 0.7050 (ttm) cc_final: 0.6840 (ttm) REVERT: A 244 ASN cc_start: 0.8061 (m-40) cc_final: 0.7783 (m110) REVERT: B 59 TYR cc_start: 0.8031 (m-80) cc_final: 0.7153 (m-80) REVERT: B 214 ARG cc_start: 0.7952 (mpt180) cc_final: 0.7420 (ttp80) REVERT: B 217 MET cc_start: 0.7244 (mtt) cc_final: 0.6623 (ptp) REVERT: B 277 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (m) REVERT: N 236 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.5322 (t80) REVERT: G 38 MET cc_start: 0.6923 (mmm) cc_final: 0.6650 (mmm) REVERT: R 22 ARG cc_start: 0.4255 (mmp-170) cc_final: 0.2871 (mtm-85) REVERT: R 24 ARG cc_start: 0.7253 (mtp85) cc_final: 0.6897 (mtp180) REVERT: R 25 PHE cc_start: 0.7293 (t80) cc_final: 0.6430 (t80) REVERT: R 101 THR cc_start: 0.7005 (m) cc_final: 0.6796 (p) REVERT: R 118 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5913 (mtp) REVERT: R 137 MET cc_start: 0.7342 (tmm) cc_final: 0.7134 (tmm) REVERT: R 290 GLN cc_start: 0.6352 (tp40) cc_final: 0.5917 (tp40) outliers start: 33 outliers final: 24 residues processed: 169 average time/residue: 0.1043 time to fit residues: 24.0355 Evaluate side-chains 155 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115229 restraints weight = 10095.502| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.99 r_work: 0.3177 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9221 Z= 0.193 Angle : 0.639 13.584 12508 Z= 0.329 Chirality : 0.044 0.236 1438 Planarity : 0.005 0.064 1589 Dihedral : 5.875 51.676 1279 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.80 % Allowed : 18.79 % Favored : 77.41 % 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 aren not related in a simple way. whole: -0.47 (0.25), residues: 1141 helix: 0.83 (0.27), residues: 383 sheet: -0.59 (0.32), residues: 271 loop : -0.99 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.018 0.002 TYR N 236 PHE 0.018 0.002 PHE R 27 TRP 0.022 0.002 TRP B 211 HIS 0.005 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9218) covalent geometry : angle 0.63817 (12502) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.20145 ( 6) hydrogen bonds : bond 0.04660 ( 445) hydrogen bonds : angle 4.83616 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7583 (mttp) cc_final: 0.7375 (mttp) REVERT: A 199 ASP cc_start: 0.6943 (m-30) cc_final: 0.6633 (m-30) REVERT: B 59 TYR cc_start: 0.8259 (m-80) cc_final: 0.7416 (m-80) REVERT: B 197 ARG cc_start: 0.7588 (mmt180) cc_final: 0.7259 (mmt180) REVERT: B 214 ARG cc_start: 0.7973 (mpt180) cc_final: 0.7225 (ttp80) REVERT: N 74 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: N 87 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7729 (ptp-170) REVERT: N 236 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5407 (t80) REVERT: R 22 ARG cc_start: 0.4606 (mmp-170) cc_final: 0.3378 (mtm-85) REVERT: R 25 PHE cc_start: 0.7406 (t80) cc_final: 0.6458 (t80) REVERT: R 137 MET cc_start: 0.7124 (tmm) cc_final: 0.6831 (tmm) REVERT: R 215 ASN cc_start: 0.8228 (m-40) cc_final: 0.7617 (m-40) outliers start: 37 outliers final: 25 residues processed: 173 average time/residue: 0.1061 time to fit residues: 25.1416 Evaluate side-chains 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.0040 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 57 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115754 restraints weight = 10172.595| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.00 r_work: 0.3180 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9221 Z= 0.152 Angle : 0.596 11.296 12508 Z= 0.305 Chirality : 0.043 0.202 1438 Planarity : 0.004 0.057 1589 Dihedral : 5.367 56.833 1278 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.80 % Allowed : 19.10 % Favored : 77.10 % 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 aren not related in a simple way. whole: -0.32 (0.25), residues: 1141 helix: 1.07 (0.27), residues: 384 sheet: -0.39 (0.33), residues: 257 loop : -1.08 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR N 236 PHE 0.015 0.001 PHE R 27 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9218) covalent geometry : angle 0.59580 (12502) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.00131 ( 6) hydrogen bonds : bond 0.04221 ( 445) hydrogen bonds : angle 4.67900 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.6981 (m-30) cc_final: 0.6650 (m-30) REVERT: B 59 TYR cc_start: 0.8207 (m-80) cc_final: 0.7419 (m-80) REVERT: B 191 SER cc_start: 0.8761 (t) cc_final: 0.8325 (t) REVERT: B 214 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7252 (ttp80) REVERT: N 74 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: N 161 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7307 (mtm110) REVERT: N 236 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.5293 (t80) REVERT: G 58 GLU cc_start: 0.8094 (tp30) cc_final: 0.7795 (tp30) REVERT: R 25 PHE cc_start: 0.7476 (t80) cc_final: 0.6748 (t80) REVERT: R 137 MET cc_start: 0.6964 (tmm) cc_final: 0.6703 (tmm) REVERT: R 215 ASN cc_start: 0.8213 (m-40) cc_final: 0.7523 (m-40) outliers start: 37 outliers final: 24 residues processed: 172 average time/residue: 0.1029 time to fit residues: 24.2711 Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.170913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113491 restraints weight = 10144.429| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.89 r_work: 0.3148 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9221 Z= 0.199 Angle : 0.630 10.330 12508 Z= 0.324 Chirality : 0.044 0.238 1438 Planarity : 0.004 0.061 1589 Dihedral : 5.181 57.238 1276 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.83 % Allowed : 18.28 % Favored : 76.90 % 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 aren not related in a simple way. whole: -0.45 (0.25), residues: 1141 helix: 1.00 (0.26), residues: 384 sheet: -0.82 (0.31), residues: 278 loop : -0.95 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.018 0.002 TYR N 236 PHE 0.023 0.002 PHE R 303 TRP 0.017 0.002 TRP B 211 HIS 0.006 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9218) covalent geometry : angle 0.63029 (12502) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.88690 ( 6) hydrogen bonds : bond 0.04418 ( 445) hydrogen bonds : angle 4.72067 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7915 (m-30) cc_final: 0.7664 (m-30) REVERT: A 199 ASP cc_start: 0.6991 (m-30) cc_final: 0.6653 (m-30) REVERT: B 304 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8409 (ttp-170) REVERT: N 161 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7386 (mtm110) REVERT: N 236 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5594 (t80) REVERT: R 25 PHE cc_start: 0.7440 (t80) cc_final: 0.6786 (t80) REVERT: R 215 ASN cc_start: 0.8223 (m-40) cc_final: 0.7499 (m-40) outliers start: 47 outliers final: 34 residues processed: 174 average time/residue: 0.1103 time to fit residues: 26.2485 Evaluate side-chains 168 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116869 restraints weight = 10134.860| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.94 r_work: 0.3189 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9221 Z= 0.124 Angle : 0.577 11.305 12508 Z= 0.292 Chirality : 0.042 0.186 1438 Planarity : 0.004 0.060 1589 Dihedral : 4.916 58.734 1274 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.29 % Allowed : 19.82 % Favored : 76.90 % 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 aren not related in a simple way. whole: -0.27 (0.25), residues: 1141 helix: 1.18 (0.26), residues: 387 sheet: -0.53 (0.32), residues: 273 loop : -1.03 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.012 0.001 TYR N 191 PHE 0.020 0.001 PHE R 303 TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9218) covalent geometry : angle 0.57639 (12502) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.85246 ( 6) hydrogen bonds : bond 0.03934 ( 445) hydrogen bonds : angle 4.55645 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7805 (m-30) cc_final: 0.7518 (m-30) REVERT: A 75 GLN cc_start: 0.7481 (pp30) cc_final: 0.7280 (pp30) REVERT: A 199 ASP cc_start: 0.6931 (m-30) cc_final: 0.6582 (m-30) REVERT: A 241 ARG cc_start: 0.6810 (mpt180) cc_final: 0.6553 (mpt180) REVERT: B 134 ARG cc_start: 0.7770 (ptt-90) cc_final: 0.7564 (ptt-90) REVERT: B 191 SER cc_start: 0.8779 (t) cc_final: 0.8383 (t) REVERT: N 161 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7332 (mtm110) REVERT: N 236 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.5015 (t80) REVERT: R 25 PHE cc_start: 0.7408 (t80) cc_final: 0.6753 (t80) REVERT: R 118 MET cc_start: 0.6032 (ttp) cc_final: 0.5650 (mtp) REVERT: R 137 MET cc_start: 0.6789 (tmm) cc_final: 0.6529 (tmm) REVERT: R 215 ASN cc_start: 0.8098 (m-40) cc_final: 0.7397 (m-40) outliers start: 32 outliers final: 26 residues processed: 167 average time/residue: 0.1014 time to fit residues: 23.1367 Evaluate side-chains 166 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118202 restraints weight = 10153.977| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.91 r_work: 0.3208 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9221 Z= 0.116 Angle : 0.563 11.476 12508 Z= 0.285 Chirality : 0.041 0.172 1438 Planarity : 0.004 0.061 1589 Dihedral : 4.741 57.616 1274 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.11 % Allowed : 19.40 % Favored : 76.49 % 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 aren not related in a simple way. whole: -0.11 (0.25), residues: 1141 helix: 1.32 (0.26), residues: 390 sheet: -0.48 (0.32), residues: 272 loop : -0.94 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.010 0.001 TYR N 191 PHE 0.017 0.001 PHE R 303 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9218) covalent geometry : angle 0.56311 (12502) SS BOND : bond 0.00393 ( 3) SS BOND : angle 0.70680 ( 6) hydrogen bonds : bond 0.03773 ( 445) hydrogen bonds : angle 4.43998 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.6965 (m-30) cc_final: 0.6601 (m-30) REVERT: A 241 ARG cc_start: 0.6873 (mpt180) cc_final: 0.6630 (mpt180) REVERT: B 191 SER cc_start: 0.8767 (t) cc_final: 0.8315 (t) REVERT: B 214 ARG cc_start: 0.7948 (mpt180) cc_final: 0.7625 (mmt-90) REVERT: N 67 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7407 (mtm110) REVERT: N 161 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7338 (mtm110) REVERT: N 221 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6434 (mm-30) REVERT: R 25 PHE cc_start: 0.7436 (t80) cc_final: 0.6793 (t80) REVERT: R 118 MET cc_start: 0.6094 (ttp) cc_final: 0.5788 (mtp) REVERT: R 215 ASN cc_start: 0.8066 (m-40) cc_final: 0.7355 (m-40) outliers start: 40 outliers final: 32 residues processed: 175 average time/residue: 0.1130 time to fit residues: 26.6992 Evaluate side-chains 167 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117725 restraints weight = 10072.565| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.92 r_work: 0.3205 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9221 Z= 0.123 Angle : 0.564 11.999 12508 Z= 0.286 Chirality : 0.042 0.171 1438 Planarity : 0.004 0.059 1589 Dihedral : 4.699 55.266 1274 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.59 % Allowed : 20.02 % Favored : 76.39 % 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 aren not related in a simple way. whole: -0.01 (0.25), residues: 1141 helix: 1.42 (0.26), residues: 390 sheet: -0.43 (0.32), residues: 270 loop : -0.90 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.010 0.001 TYR N 191 PHE 0.015 0.001 PHE R 303 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9218) covalent geometry : angle 0.56386 (12502) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.65442 ( 6) hydrogen bonds : bond 0.03768 ( 445) hydrogen bonds : angle 4.43970 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6773 (ptp90) REVERT: A 199 ASP cc_start: 0.7095 (m-30) cc_final: 0.6728 (m-30) REVERT: A 241 ARG cc_start: 0.6949 (mpt180) cc_final: 0.6702 (mpt180) REVERT: B 59 TYR cc_start: 0.8188 (m-80) cc_final: 0.7212 (m-80) REVERT: B 191 SER cc_start: 0.8804 (t) cc_final: 0.8468 (t) REVERT: N 18 ARG cc_start: 0.7949 (tpt-90) cc_final: 0.7705 (tpt-90) REVERT: N 67 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7329 (mtm110) REVERT: N 161 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7339 (mtm110) REVERT: N 236 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4992 (t80) REVERT: R 25 PHE cc_start: 0.7453 (t80) cc_final: 0.6824 (t80) REVERT: R 118 MET cc_start: 0.6191 (ttp) cc_final: 0.5868 (mtp) REVERT: R 215 ASN cc_start: 0.7982 (m-40) cc_final: 0.7294 (m-40) outliers start: 35 outliers final: 32 residues processed: 171 average time/residue: 0.1145 time to fit residues: 26.2073 Evaluate side-chains 172 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112193 restraints weight = 10097.108| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.91 r_work: 0.3143 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9221 Z= 0.212 Angle : 0.634 12.195 12508 Z= 0.324 Chirality : 0.044 0.239 1438 Planarity : 0.004 0.059 1589 Dihedral : 5.007 53.360 1274 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.11 % Allowed : 19.71 % Favored : 76.18 % 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 aren not related in a simple way. whole: -0.20 (0.25), residues: 1141 helix: 1.23 (0.26), residues: 390 sheet: -0.68 (0.31), residues: 274 loop : -0.87 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.016 0.002 TYR N 236 PHE 0.014 0.002 PHE R 27 TRP 0.015 0.002 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9218) covalent geometry : angle 0.63359 (12502) SS BOND : bond 0.00425 ( 3) SS BOND : angle 0.71505 ( 6) hydrogen bonds : bond 0.04391 ( 445) hydrogen bonds : angle 4.64990 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6806 (ptp90) REVERT: A 199 ASP cc_start: 0.7146 (m-30) cc_final: 0.6840 (m-30) REVERT: B 214 ARG cc_start: 0.7928 (mpt180) cc_final: 0.7402 (mmt-90) REVERT: B 304 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8385 (ttp-170) REVERT: N 161 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7388 (mtm110) REVERT: N 203 ARG cc_start: 0.6660 (ptp90) cc_final: 0.6457 (ptt-90) REVERT: N 221 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6489 (mm-30) REVERT: N 236 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5704 (t80) REVERT: G 38 MET cc_start: 0.7687 (mtp) cc_final: 0.7445 (mtm) REVERT: G 58 GLU cc_start: 0.8554 (tp30) cc_final: 0.8322 (tp30) REVERT: R 25 PHE cc_start: 0.7386 (t80) cc_final: 0.6762 (t80) REVERT: R 118 MET cc_start: 0.6321 (ttp) cc_final: 0.5840 (mtp) REVERT: R 215 ASN cc_start: 0.8202 (m-40) cc_final: 0.7515 (m-40) outliers start: 40 outliers final: 35 residues processed: 175 average time/residue: 0.1045 time to fit residues: 24.5081 Evaluate side-chains 169 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.174237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115513 restraints weight = 10202.119| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.00 r_work: 0.3159 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9221 Z= 0.152 Angle : 0.593 12.194 12508 Z= 0.301 Chirality : 0.043 0.210 1438 Planarity : 0.004 0.059 1589 Dihedral : 4.838 49.900 1274 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.90 % Allowed : 19.92 % Favored : 76.18 % 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 aren not related in a simple way. whole: -0.12 (0.25), residues: 1141 helix: 1.35 (0.26), residues: 391 sheet: -0.65 (0.32), residues: 274 loop : -0.85 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.014 0.001 TYR N 236 PHE 0.014 0.001 PHE R 303 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9218) covalent geometry : angle 0.59291 (12502) SS BOND : bond 0.00343 ( 3) SS BOND : angle 0.64642 ( 6) hydrogen bonds : bond 0.04031 ( 445) hydrogen bonds : angle 4.56340 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6790 (ptp90) REVERT: A 199 ASP cc_start: 0.7015 (m-30) cc_final: 0.6642 (m-30) REVERT: A 241 ARG cc_start: 0.6915 (mpt180) cc_final: 0.6621 (mpt180) REVERT: B 191 SER cc_start: 0.8733 (t) cc_final: 0.8410 (t) REVERT: N 161 ARG cc_start: 0.7734 (ttp-110) cc_final: 0.7311 (mtm110) REVERT: N 221 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6620 (mm-30) REVERT: N 236 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.5236 (t80) REVERT: R 25 PHE cc_start: 0.7418 (t80) cc_final: 0.6782 (t80) REVERT: R 118 MET cc_start: 0.6271 (ttp) cc_final: 0.5847 (mtp) REVERT: R 215 ASN cc_start: 0.8112 (m-40) cc_final: 0.7428 (m-40) outliers start: 38 outliers final: 36 residues processed: 171 average time/residue: 0.1150 time to fit residues: 26.4232 Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.176011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118183 restraints weight = 9930.108| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.88 r_work: 0.3204 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9221 Z= 0.117 Angle : 0.563 12.315 12508 Z= 0.285 Chirality : 0.041 0.172 1438 Planarity : 0.004 0.061 1589 Dihedral : 4.618 49.136 1274 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.00 % Allowed : 20.23 % Favored : 75.77 % 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 aren not related in a simple way. whole: 0.01 (0.26), residues: 1141 helix: 1.51 (0.27), residues: 391 sheet: -0.64 (0.32), residues: 267 loop : -0.80 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.011 0.001 TYR N 191 PHE 0.014 0.001 PHE R 303 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9218) covalent geometry : angle 0.56337 (12502) SS BOND : bond 0.00300 ( 3) SS BOND : angle 0.54488 ( 6) hydrogen bonds : bond 0.03703 ( 445) hydrogen bonds : angle 4.43199 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.06 seconds wall clock time: 45 minutes 5.12 seconds (2705.12 seconds total)