Starting phenix.real_space_refine on Wed Sep 17 14:23:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgo_38329/09_2025/8xgo_38329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgo_38329/09_2025/8xgo_38329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xgo_38329/09_2025/8xgo_38329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgo_38329/09_2025/8xgo_38329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xgo_38329/09_2025/8xgo_38329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgo_38329/09_2025/8xgo_38329.map" } resolution = 2.68 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= -0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5754 2.51 5 N 1568 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9045 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2309 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 18, 'TRANS': 280} Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1880 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'ACE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UYA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {'XZA': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 2, None: 2} Not linked: pdbres="PHE F 6 " pdbres="XZA F 7 " Not linked: pdbres="XZA F 7 " pdbres="LEU F 8 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'XZA:plan-1': 1, 'NMM:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 9045 At special positions: 0 Unit cell: (88.81, 122.84, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1664 8.00 N 1568 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 113 " 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=3, symmetry=0 Links applied TRANS " DTH F 5 " - " ASN F 4 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 337.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB UYA F 3 " pdb=" CB PHE F 6 " Input residue name is d-peptide pdb=" CB DTH F 5 " Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.2% alpha, 20.3% 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 39 through 45 removed outlier: 4.230A pdb=" N TRP A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 70 removed outlier: 3.746A pdb=" N PHE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 102 Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 111 through 146 removed outlier: 3.620A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.303A pdb=" N HIS A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 197 through 213 Processing helix chain 'A' and resid 213 through 236 removed outlier: 4.170A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 288 removed outlier: 3.503A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.755A pdb=" N SER A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.556A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'E' and resid 6 through 31 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 206 through 215 removed outlier: 4.364A pdb=" N ILE E 211 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS E 212 " --> pdb=" O LYS E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 240 through 247 removed outlier: 3.501A pdb=" N GLU E 244 " --> pdb=" O ASN E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 254 Processing helix chain 'E' and resid 269 through 277 Processing helix chain 'E' and resid 281 through 286 removed outlier: 4.048A pdb=" N TYR E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 309 Processing helix chain 'E' and resid 329 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.806A pdb=" N TYR A 190 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.353A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.618A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.922A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.478A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.727A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.667A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AB1, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB2, first strand: chain 'D' and resid 62 through 63 Processing sheet with id=AB3, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AB4, first strand: chain 'D' and resid 211 through 212 removed outlier: 6.518A pdb=" N TRP D 193 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR D 207 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 191 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 242 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 189 removed outlier: 6.951A pdb=" N LEU E 36 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER E 219 " --> pdb=" O LYS E 35 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1260 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: 1.47 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1451 1.30 - 1.43: 2495 1.43 - 1.56: 5192 1.56 - 1.69: 17 1.69 - 1.82: 87 Bond restraints: 9242 Sorted by residual: bond pdb=" C NMM F 9 " pdb=" N TRP F 10 " ideal model delta sigma weight residual 1.329 1.508 -0.179 1.40e-02 5.10e+03 1.64e+02 bond pdb=" C UYA F 3 " pdb=" N ASN F 4 " ideal model delta sigma weight residual 1.329 1.492 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" C LEU F 8 " pdb=" N NMM F 9 " ideal model delta sigma weight residual 1.329 1.476 -0.147 1.40e-02 5.10e+03 1.11e+02 bond pdb=" C DTH F 5 " pdb=" N PHE F 6 " ideal model delta sigma weight residual 1.329 1.473 -0.144 1.40e-02 5.10e+03 1.06e+02 bond pdb=" CB UYA F 3 " pdb=" CG UYA F 3 " ideal model delta sigma weight residual 1.518 1.343 0.175 2.00e-02 2.50e+03 7.67e+01 ... (remaining 9237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 12431 3.07 - 6.15: 94 6.15 - 9.22: 7 9.22 - 12.30: 1 12.30 - 15.37: 1 Bond angle restraints: 12534 Sorted by residual: angle pdb=" CA ASN F 4 " pdb=" CB ASN F 4 " pdb=" CG ASN F 4 " ideal model delta sigma weight residual 112.60 120.96 -8.36 1.00e+00 1.00e+00 6.99e+01 angle pdb=" C LEU E 310 " pdb=" N ASN E 311 " pdb=" CA ASN E 311 " ideal model delta sigma weight residual 121.80 137.17 -15.37 2.44e+00 1.68e-01 3.97e+01 angle pdb=" CA DTH F 5 " pdb=" C DTH F 5 " pdb=" N PHE F 6 " ideal model delta sigma weight residual 116.20 126.56 -10.36 2.00e+00 2.50e-01 2.68e+01 angle pdb=" O DTH F 5 " pdb=" C DTH F 5 " pdb=" N PHE F 6 " ideal model delta sigma weight residual 123.00 117.04 5.96 1.60e+00 3.91e-01 1.39e+01 angle pdb=" C ARG D 208 " pdb=" N MET D 209 " pdb=" CA MET D 209 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4993 17.43 - 34.85: 404 34.85 - 52.28: 58 52.28 - 69.70: 14 69.70 - 87.13: 12 Dihedral angle restraints: 5481 sinusoidal: 2130 harmonic: 3351 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA LEU E 310 " pdb=" C LEU E 310 " pdb=" N ASN E 311 " pdb=" CA ASN E 311 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LYS E 246 " pdb=" C LYS E 246 " pdb=" N ALA E 247 " pdb=" CA ALA E 247 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 1411 1.006 - 2.012: 0 2.012 - 3.018: 0 3.018 - 4.025: 0 4.025 - 5.031: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA PHE F 6 " pdb=" N PHE F 6 " pdb=" C PHE F 6 " pdb=" CB PHE F 6 " both_signs ideal model delta sigma weight residual False 2.51 -2.52 5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" CA UYA F 3 " pdb=" N UYA F 3 " pdb=" C UYA F 3 " pdb=" CB UYA F 3 " both_signs ideal model delta sigma weight residual False -2.48 -3.23 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA LEU F 8 " pdb=" N LEU F 8 " pdb=" C LEU F 8 " pdb=" CB LEU F 8 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 1409 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 248 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU E 248 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU E 248 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE E 249 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 48 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C PHE A 48 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE A 48 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE A 49 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 167 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 168 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 168 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 168 " -0.025 5.00e-02 4.00e+02 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 245 2.70 - 3.25: 9031 3.25 - 3.80: 14728 3.80 - 4.35: 19516 4.35 - 4.90: 32622 Nonbonded interactions: 76142 Sorted by model distance: nonbonded pdb=" OD2 ASP D 90 " pdb=" NZ LYS D 93 " model vdw 2.144 3.120 nonbonded pdb=" NH1 ARG B 22 " pdb=" OD2 ASP B 258 " model vdw 2.157 3.120 nonbonded pdb=" O LEU A 57 " pdb=" OG SER A 61 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR D 192 " pdb=" OE2 GLU E 8 " model vdw 2.210 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.211 3.120 ... (remaining 76137 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: 3.110 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.179 9248 Z= 0.431 Angle : 0.679 15.370 12541 Z= 0.366 Chirality : 0.143 5.031 1412 Planarity : 0.004 0.045 1593 Dihedral : 13.277 87.130 3312 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.06 (0.26), residues: 1133 helix: 1.54 (0.27), residues: 396 sheet: -0.45 (0.32), residues: 255 loop : -1.12 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.019 0.001 TYR A 313 PHE 0.010 0.001 PHE C 61 TRP 0.010 0.001 TRP D 193 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00742 ( 9242) covalent geometry : angle 0.67810 (12534) SS BOND : bond 0.00110 ( 2) SS BOND : angle 1.30638 ( 4) hydrogen bonds : bond 0.11889 ( 447) hydrogen bonds : angle 5.38397 ( 1260) Misc. bond : bond 0.03240 ( 3) link_TRANS : bond 0.17294 ( 1) link_TRANS : angle 2.24996 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.222 Fit side-chains REVERT: A 332 GLN cc_start: 0.8336 (pp30) cc_final: 0.7999 (pp30) REVERT: D 240 ASP cc_start: 0.8411 (m-30) cc_final: 0.7945 (m-30) REVERT: D 241 VAL cc_start: 0.9270 (t) cc_final: 0.8993 (p) REVERT: E 231 GLN cc_start: 0.8834 (mm110) cc_final: 0.8470 (mm110) REVERT: E 259 GLN cc_start: 0.8726 (mm110) cc_final: 0.8487 (mm110) REVERT: E 315 ASP cc_start: 0.7959 (p0) cc_final: 0.7713 (p0) REVERT: F 6 PHE cc_start: 0.8087 (m-80) cc_final: 0.7864 (m-80) outliers start: 2 outliers final: 1 residues processed: 184 average time/residue: 0.6887 time to fit residues: 133.1447 Evaluate side-chains 146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN A 286 GLN B 44 GLN B 75 GLN D 99 GLN D 203 GLN E 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.067049 restraints weight = 17175.093| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.92 r_work: 0.2744 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9248 Z= 0.169 Angle : 0.654 11.075 12541 Z= 0.331 Chirality : 0.045 0.401 1412 Planarity : 0.005 0.046 1593 Dihedral : 5.487 62.558 1274 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.96 % Allowed : 11.16 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1133 helix: 1.64 (0.27), residues: 400 sheet: -0.55 (0.31), residues: 270 loop : -1.09 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.033 0.001 TYR A 313 PHE 0.021 0.001 PHE F 6 TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9242) covalent geometry : angle 0.65298 (12534) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.42433 ( 4) hydrogen bonds : bond 0.03882 ( 447) hydrogen bonds : angle 4.68265 ( 1260) Misc. bond : bond 0.00078 ( 3) link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 2.48638 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.216 Fit side-chains REVERT: B 217 MET cc_start: 0.7719 (ptm) cc_final: 0.7107 (pp-130) REVERT: C 21 MET cc_start: 0.8710 (tmm) cc_final: 0.8178 (tmm) REVERT: D 28 LEU cc_start: 0.9173 (tt) cc_final: 0.8896 (tm) REVERT: D 99 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8444 (tp40) REVERT: D 240 ASP cc_start: 0.8529 (m-30) cc_final: 0.8157 (m-30) REVERT: E 43 GLU cc_start: 0.8480 (pt0) cc_final: 0.7787 (pp20) REVERT: E 231 GLN cc_start: 0.8795 (mm110) cc_final: 0.8204 (mm110) REVERT: E 259 GLN cc_start: 0.9106 (mm110) cc_final: 0.8875 (mm110) REVERT: E 327 ASP cc_start: 0.8459 (t0) cc_final: 0.8158 (t0) outliers start: 19 outliers final: 6 residues processed: 164 average time/residue: 0.6070 time to fit residues: 105.0530 Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN B 44 GLN B 156 GLN D 99 GLN D 203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.064062 restraints weight = 17186.098| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.87 r_work: 0.2685 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9248 Z= 0.268 Angle : 0.683 10.285 12541 Z= 0.348 Chirality : 0.047 0.369 1412 Planarity : 0.005 0.042 1593 Dihedral : 5.829 69.810 1274 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.38 % Allowed : 15.50 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.07 (0.26), residues: 1133 helix: 1.69 (0.27), residues: 392 sheet: -0.58 (0.31), residues: 268 loop : -1.20 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 27 TYR 0.026 0.002 TYR A 103 PHE 0.013 0.002 PHE A 48 TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 9242) covalent geometry : angle 0.68121 (12534) SS BOND : bond 0.00279 ( 2) SS BOND : angle 1.57982 ( 4) hydrogen bonds : bond 0.04301 ( 447) hydrogen bonds : angle 4.72883 ( 1260) Misc. bond : bond 0.00090 ( 3) link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 2.32988 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.387 Fit side-chains REVERT: A 54 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8950 (mm) REVERT: B 19 ARG cc_start: 0.8889 (ttp-110) cc_final: 0.8443 (ttp-110) REVERT: B 32 GLN cc_start: 0.8498 (pm20) cc_final: 0.8204 (pm20) REVERT: B 44 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8498 (mm-40) REVERT: B 217 MET cc_start: 0.8059 (ptm) cc_final: 0.7651 (ppp) REVERT: B 260 GLU cc_start: 0.8236 (tp30) cc_final: 0.7921 (tp30) REVERT: C 21 MET cc_start: 0.8693 (tmm) cc_final: 0.8261 (tmm) REVERT: C 36 ASP cc_start: 0.8711 (m-30) cc_final: 0.8478 (m-30) REVERT: D 28 LEU cc_start: 0.9145 (tt) cc_final: 0.8856 (tm) REVERT: D 240 ASP cc_start: 0.8541 (m-30) cc_final: 0.8197 (m-30) REVERT: E 43 GLU cc_start: 0.8438 (pt0) cc_final: 0.7823 (pp20) REVERT: E 191 GLN cc_start: 0.8467 (pp30) cc_final: 0.8252 (pp30) REVERT: E 231 GLN cc_start: 0.8770 (mm110) cc_final: 0.8139 (mm110) outliers start: 23 outliers final: 10 residues processed: 156 average time/residue: 0.6265 time to fit residues: 103.2537 Evaluate side-chains 146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.066110 restraints weight = 16891.596| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.00 r_work: 0.2723 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9248 Z= 0.141 Angle : 0.623 9.619 12541 Z= 0.313 Chirality : 0.043 0.326 1412 Planarity : 0.004 0.039 1593 Dihedral : 5.515 69.620 1274 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 17.36 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1133 helix: 1.83 (0.27), residues: 391 sheet: -0.57 (0.31), residues: 268 loop : -1.18 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.018 0.001 TYR A 103 PHE 0.020 0.001 PHE A 48 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9242) covalent geometry : angle 0.62174 (12534) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.48371 ( 4) hydrogen bonds : bond 0.03519 ( 447) hydrogen bonds : angle 4.53134 ( 1260) Misc. bond : bond 0.00038 ( 3) link_TRANS : bond 0.00056 ( 1) link_TRANS : angle 2.07553 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.364 Fit side-chains REVERT: A 54 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 73 MET cc_start: 0.8874 (mmm) cc_final: 0.8432 (mtp) REVERT: B 19 ARG cc_start: 0.8904 (ttp-110) cc_final: 0.8477 (ttp-110) REVERT: B 44 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8395 (mm-40) REVERT: B 217 MET cc_start: 0.8089 (ptm) cc_final: 0.7735 (ppp) REVERT: B 260 GLU cc_start: 0.8128 (tp30) cc_final: 0.7917 (tp30) REVERT: C 21 MET cc_start: 0.8681 (tmm) cc_final: 0.8202 (tmm) REVERT: C 36 ASP cc_start: 0.8698 (m-30) cc_final: 0.8409 (m-30) REVERT: C 47 GLU cc_start: 0.8534 (mp0) cc_final: 0.8324 (mp0) REVERT: D 28 LEU cc_start: 0.9118 (tt) cc_final: 0.8830 (tm) REVERT: D 240 ASP cc_start: 0.8510 (m-30) cc_final: 0.8279 (m-30) REVERT: E 43 GLU cc_start: 0.8440 (pt0) cc_final: 0.7771 (pp20) REVERT: E 231 GLN cc_start: 0.8747 (mm110) cc_final: 0.8064 (mm110) REVERT: E 289 TYR cc_start: 0.8685 (t80) cc_final: 0.8397 (t80) REVERT: E 327 ASP cc_start: 0.8487 (t0) cc_final: 0.8226 (t0) outliers start: 26 outliers final: 11 residues processed: 165 average time/residue: 0.5910 time to fit residues: 103.2582 Evaluate side-chains 156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 315 ASN D 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.066943 restraints weight = 17110.668| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.92 r_work: 0.2750 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9248 Z= 0.140 Angle : 0.617 9.351 12541 Z= 0.312 Chirality : 0.043 0.319 1412 Planarity : 0.004 0.040 1593 Dihedral : 5.299 68.723 1274 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.89 % Allowed : 17.98 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.10 (0.26), residues: 1133 helix: 1.87 (0.27), residues: 392 sheet: -0.47 (0.32), residues: 266 loop : -1.14 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 27 TYR 0.015 0.001 TYR A 103 PHE 0.021 0.001 PHE A 48 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9242) covalent geometry : angle 0.61607 (12534) SS BOND : bond 0.00354 ( 2) SS BOND : angle 1.43605 ( 4) hydrogen bonds : bond 0.03443 ( 447) hydrogen bonds : angle 4.43477 ( 1260) Misc. bond : bond 0.00036 ( 3) link_TRANS : bond 0.00090 ( 1) link_TRANS : angle 2.08296 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.324 Fit side-chains REVERT: A 54 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8941 (mm) REVERT: A 73 MET cc_start: 0.8857 (mmm) cc_final: 0.8610 (mtm) REVERT: A 114 MET cc_start: 0.8407 (tpp) cc_final: 0.8199 (tpp) REVERT: B 19 ARG cc_start: 0.8921 (ttp-110) cc_final: 0.8498 (ttp-110) REVERT: B 32 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: B 44 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8347 (mm-40) REVERT: B 217 MET cc_start: 0.8149 (ptm) cc_final: 0.7789 (ppp) REVERT: C 21 MET cc_start: 0.8727 (tmm) cc_final: 0.8327 (tmm) REVERT: C 36 ASP cc_start: 0.8742 (m-30) cc_final: 0.8470 (m-30) REVERT: C 47 GLU cc_start: 0.8544 (mp0) cc_final: 0.8275 (mp0) REVERT: D 36 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8896 (tppp) REVERT: D 99 GLN cc_start: 0.8589 (tp40) cc_final: 0.8225 (tp40) REVERT: D 100 MET cc_start: 0.9245 (mtm) cc_final: 0.8997 (mtm) REVERT: D 240 ASP cc_start: 0.8496 (m-30) cc_final: 0.8293 (m-30) REVERT: E 43 GLU cc_start: 0.8414 (pt0) cc_final: 0.7780 (pp20) REVERT: E 231 GLN cc_start: 0.8753 (mm110) cc_final: 0.8104 (mm110) REVERT: E 289 TYR cc_start: 0.8700 (t80) cc_final: 0.8439 (t80) REVERT: E 327 ASP cc_start: 0.8489 (t0) cc_final: 0.8229 (t0) outliers start: 28 outliers final: 15 residues processed: 164 average time/residue: 0.6015 time to fit residues: 104.5205 Evaluate side-chains 163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.065109 restraints weight = 17204.000| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.92 r_work: 0.2712 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9248 Z= 0.207 Angle : 0.653 9.805 12541 Z= 0.330 Chirality : 0.045 0.328 1412 Planarity : 0.004 0.041 1593 Dihedral : 5.421 68.908 1274 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.00 % Allowed : 18.29 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.05 (0.26), residues: 1133 helix: 1.81 (0.27), residues: 392 sheet: -0.52 (0.31), residues: 268 loop : -1.13 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 27 TYR 0.026 0.001 TYR A 103 PHE 0.018 0.001 PHE A 48 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9242) covalent geometry : angle 0.65209 (12534) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.44671 ( 4) hydrogen bonds : bond 0.03771 ( 447) hydrogen bonds : angle 4.47610 ( 1260) Misc. bond : bond 0.00055 ( 3) link_TRANS : bond 0.00047 ( 1) link_TRANS : angle 2.06982 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8971 (mm) REVERT: A 73 MET cc_start: 0.8930 (mmm) cc_final: 0.8690 (mtp) REVERT: B 19 ARG cc_start: 0.8933 (ttp-110) cc_final: 0.8512 (ttp-110) REVERT: B 32 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: B 44 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8411 (mm-40) REVERT: B 217 MET cc_start: 0.8212 (ptm) cc_final: 0.7836 (ppp) REVERT: C 21 MET cc_start: 0.8724 (tmm) cc_final: 0.8328 (tmm) REVERT: C 36 ASP cc_start: 0.8771 (m-30) cc_final: 0.8492 (m-30) REVERT: C 47 GLU cc_start: 0.8559 (mp0) cc_final: 0.8281 (mp0) REVERT: D 28 LEU cc_start: 0.9098 (tt) cc_final: 0.8834 (tm) REVERT: D 240 ASP cc_start: 0.8495 (m-30) cc_final: 0.8280 (m-30) REVERT: E 43 GLU cc_start: 0.8395 (pt0) cc_final: 0.7760 (pp20) REVERT: E 231 GLN cc_start: 0.8728 (mm110) cc_final: 0.8090 (mm110) REVERT: E 275 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8657 (mm-30) REVERT: E 289 TYR cc_start: 0.8755 (t80) cc_final: 0.8489 (t80) REVERT: E 327 ASP cc_start: 0.8513 (t0) cc_final: 0.8208 (t0) outliers start: 29 outliers final: 16 residues processed: 163 average time/residue: 0.5900 time to fit residues: 101.8738 Evaluate side-chains 157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067580 restraints weight = 17025.365| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.91 r_work: 0.2762 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9248 Z= 0.131 Angle : 0.632 9.385 12541 Z= 0.316 Chirality : 0.043 0.308 1412 Planarity : 0.004 0.042 1593 Dihedral : 5.171 67.538 1274 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.79 % Allowed : 19.42 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.13 (0.26), residues: 1133 helix: 1.89 (0.27), residues: 392 sheet: -0.45 (0.32), residues: 268 loop : -1.12 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 27 TYR 0.021 0.001 TYR A 103 PHE 0.018 0.001 PHE A 48 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9242) covalent geometry : angle 0.63073 (12534) SS BOND : bond 0.00362 ( 2) SS BOND : angle 1.37681 ( 4) hydrogen bonds : bond 0.03321 ( 447) hydrogen bonds : angle 4.37349 ( 1260) Misc. bond : bond 0.00027 ( 3) link_TRANS : bond 0.00100 ( 1) link_TRANS : angle 2.03341 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.376 Fit side-chains REVERT: A 54 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 73 MET cc_start: 0.8801 (mmm) cc_final: 0.8598 (mtm) REVERT: B 19 ARG cc_start: 0.8929 (ttp-110) cc_final: 0.8508 (ttp-110) REVERT: B 32 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: B 44 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8346 (mm-40) REVERT: B 217 MET cc_start: 0.8214 (ptm) cc_final: 0.7868 (ppp) REVERT: C 21 MET cc_start: 0.8762 (tmm) cc_final: 0.8381 (tmm) REVERT: C 36 ASP cc_start: 0.8746 (m-30) cc_final: 0.8448 (m-30) REVERT: C 47 GLU cc_start: 0.8522 (mp0) cc_final: 0.8223 (mp0) REVERT: D 28 LEU cc_start: 0.9074 (tt) cc_final: 0.8799 (tm) REVERT: D 240 ASP cc_start: 0.8469 (m-30) cc_final: 0.8145 (m-30) REVERT: E 43 GLU cc_start: 0.8419 (pt0) cc_final: 0.7801 (pp20) REVERT: E 204 ARG cc_start: 0.8430 (mmp80) cc_final: 0.7932 (mmp80) REVERT: E 231 GLN cc_start: 0.8747 (mm110) cc_final: 0.8160 (mm110) REVERT: E 275 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8640 (mm-30) REVERT: E 289 TYR cc_start: 0.8724 (t80) cc_final: 0.8449 (t80) REVERT: E 327 ASP cc_start: 0.8472 (t0) cc_final: 0.8218 (t0) outliers start: 27 outliers final: 14 residues processed: 166 average time/residue: 0.5665 time to fit residues: 99.8367 Evaluate side-chains 164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.067502 restraints weight = 17080.798| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.91 r_work: 0.2761 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9248 Z= 0.142 Angle : 0.640 9.817 12541 Z= 0.320 Chirality : 0.043 0.307 1412 Planarity : 0.004 0.043 1593 Dihedral : 5.106 66.220 1274 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.17 % Allowed : 21.28 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.18 (0.26), residues: 1133 helix: 1.96 (0.27), residues: 392 sheet: -0.34 (0.32), residues: 260 loop : -1.18 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 27 TYR 0.019 0.001 TYR A 103 PHE 0.021 0.001 PHE A 48 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9242) covalent geometry : angle 0.63901 (12534) SS BOND : bond 0.00340 ( 2) SS BOND : angle 1.29336 ( 4) hydrogen bonds : bond 0.03336 ( 447) hydrogen bonds : angle 4.34019 ( 1260) Misc. bond : bond 0.00023 ( 3) link_TRANS : bond 0.00122 ( 1) link_TRANS : angle 2.06500 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8975 (mm) REVERT: A 70 HIS cc_start: 0.8481 (t-90) cc_final: 0.8258 (t-90) REVERT: B 19 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8529 (ttp-110) REVERT: B 32 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: B 44 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8326 (mm-40) REVERT: B 217 MET cc_start: 0.8245 (ptm) cc_final: 0.7879 (ppp) REVERT: C 21 MET cc_start: 0.8765 (tmm) cc_final: 0.8380 (tmm) REVERT: C 36 ASP cc_start: 0.8742 (m-30) cc_final: 0.8435 (m-30) REVERT: C 47 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: D 28 LEU cc_start: 0.9076 (tt) cc_final: 0.8803 (tm) REVERT: D 36 LYS cc_start: 0.9171 (tppt) cc_final: 0.8869 (tppp) REVERT: D 100 MET cc_start: 0.9341 (mtm) cc_final: 0.9044 (mtp) REVERT: E 43 GLU cc_start: 0.8446 (pt0) cc_final: 0.7819 (pp20) REVERT: E 204 ARG cc_start: 0.8472 (mmp80) cc_final: 0.7961 (mmp80) REVERT: E 231 GLN cc_start: 0.8726 (mm110) cc_final: 0.8156 (mm110) REVERT: E 275 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8739 (mm-30) REVERT: E 278 MET cc_start: 0.9328 (mmt) cc_final: 0.9127 (mpm) REVERT: E 289 TYR cc_start: 0.8719 (t80) cc_final: 0.8449 (t80) REVERT: E 327 ASP cc_start: 0.8436 (t0) cc_final: 0.8148 (t0) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.5718 time to fit residues: 100.0555 Evaluate side-chains 159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 89 optimal weight: 0.0030 chunk 1 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 20 GLN D 99 GLN E 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.069204 restraints weight = 17010.650| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.92 r_work: 0.2792 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9248 Z= 0.123 Angle : 0.639 10.469 12541 Z= 0.319 Chirality : 0.043 0.311 1412 Planarity : 0.004 0.045 1593 Dihedral : 4.987 64.640 1274 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.86 % Allowed : 21.90 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.24 (0.26), residues: 1133 helix: 2.00 (0.27), residues: 392 sheet: -0.31 (0.32), residues: 260 loop : -1.12 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 27 TYR 0.020 0.001 TYR A 103 PHE 0.024 0.001 PHE A 48 TRP 0.008 0.001 TRP B 63 HIS 0.002 0.000 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9242) covalent geometry : angle 0.63775 (12534) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.23073 ( 4) hydrogen bonds : bond 0.03115 ( 447) hydrogen bonds : angle 4.28286 ( 1260) Misc. bond : bond 0.00019 ( 3) link_TRANS : bond 0.00136 ( 1) link_TRANS : angle 2.06595 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8955 (mm) REVERT: A 73 MET cc_start: 0.8685 (mtp) cc_final: 0.8305 (mtm) REVERT: B 16 ASN cc_start: 0.9392 (m-40) cc_final: 0.9181 (m-40) REVERT: B 19 ARG cc_start: 0.8901 (ttp-110) cc_final: 0.8441 (ttp-110) REVERT: B 32 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: B 217 MET cc_start: 0.8231 (ptm) cc_final: 0.7885 (ppp) REVERT: C 21 MET cc_start: 0.8749 (tmm) cc_final: 0.8372 (tmm) REVERT: C 36 ASP cc_start: 0.8734 (m-30) cc_final: 0.8419 (m-30) REVERT: C 47 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: D 28 LEU cc_start: 0.9084 (tt) cc_final: 0.8813 (tm) REVERT: D 36 LYS cc_start: 0.9148 (tppt) cc_final: 0.8944 (tptm) REVERT: D 100 MET cc_start: 0.9316 (mtm) cc_final: 0.9086 (mtp) REVERT: D 235 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7794 (tpm-80) REVERT: E 17 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8426 (mmtp) REVERT: E 43 GLU cc_start: 0.8452 (pt0) cc_final: 0.7829 (pp20) REVERT: E 204 ARG cc_start: 0.8486 (mmp80) cc_final: 0.7966 (mmp80) REVERT: E 231 GLN cc_start: 0.8733 (mm110) cc_final: 0.8177 (mm110) REVERT: E 275 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8753 (mm-30) REVERT: E 289 TYR cc_start: 0.8693 (t80) cc_final: 0.8429 (t80) outliers start: 18 outliers final: 12 residues processed: 163 average time/residue: 0.5949 time to fit residues: 102.5588 Evaluate side-chains 161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 286 GLN A 315 ASN D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068537 restraints weight = 16995.681| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.92 r_work: 0.2784 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9248 Z= 0.139 Angle : 0.657 10.849 12541 Z= 0.328 Chirality : 0.044 0.304 1412 Planarity : 0.004 0.039 1593 Dihedral : 4.971 63.817 1274 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.17 % Allowed : 21.90 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.23 (0.26), residues: 1133 helix: 1.94 (0.27), residues: 399 sheet: -0.39 (0.32), residues: 272 loop : -1.09 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 27 TYR 0.018 0.001 TYR B 59 PHE 0.025 0.001 PHE A 48 TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9242) covalent geometry : angle 0.65642 (12534) SS BOND : bond 0.00345 ( 2) SS BOND : angle 1.23540 ( 4) hydrogen bonds : bond 0.03247 ( 447) hydrogen bonds : angle 4.27775 ( 1260) Misc. bond : bond 0.00022 ( 3) link_TRANS : bond 0.00141 ( 1) link_TRANS : angle 2.06202 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8960 (mm) REVERT: A 73 MET cc_start: 0.8648 (mtp) cc_final: 0.8389 (mtm) REVERT: B 16 ASN cc_start: 0.9388 (m-40) cc_final: 0.9182 (m-40) REVERT: B 19 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8439 (ttp-110) REVERT: B 217 MET cc_start: 0.8235 (ptm) cc_final: 0.7887 (ppp) REVERT: B 234 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: C 21 MET cc_start: 0.8760 (tmm) cc_final: 0.8383 (tmm) REVERT: C 36 ASP cc_start: 0.8723 (m-30) cc_final: 0.8433 (m-30) REVERT: C 47 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: D 28 LEU cc_start: 0.9088 (tt) cc_final: 0.8818 (tm) REVERT: D 100 MET cc_start: 0.9329 (mtm) cc_final: 0.9047 (mtp) REVERT: D 235 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7808 (tpm-80) REVERT: E 17 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8436 (mmtp) REVERT: E 43 GLU cc_start: 0.8453 (pt0) cc_final: 0.7834 (pp20) REVERT: E 204 ARG cc_start: 0.8471 (mmp80) cc_final: 0.7932 (mmp80) REVERT: E 215 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: E 231 GLN cc_start: 0.8722 (mm110) cc_final: 0.8172 (mm110) REVERT: E 275 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8746 (mm-30) REVERT: E 278 MET cc_start: 0.9319 (mmt) cc_final: 0.9114 (mpm) REVERT: E 289 TYR cc_start: 0.8693 (t80) cc_final: 0.8425 (t80) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 0.6211 time to fit residues: 104.4167 Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 2 TYR Chi-restraints excluded: chain F residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.066348 restraints weight = 16954.622| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.88 r_work: 0.2733 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9248 Z= 0.195 Angle : 0.680 10.723 12541 Z= 0.342 Chirality : 0.045 0.323 1412 Planarity : 0.004 0.037 1593 Dihedral : 5.179 63.467 1274 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.27 % Allowed : 22.21 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.23 (0.26), residues: 1133 helix: 1.85 (0.26), residues: 401 sheet: -0.39 (0.33), residues: 264 loop : -1.00 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.017 0.001 TYR A 65 PHE 0.027 0.001 PHE A 48 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9242) covalent geometry : angle 0.67892 (12534) SS BOND : bond 0.00400 ( 2) SS BOND : angle 1.33526 ( 4) hydrogen bonds : bond 0.03681 ( 447) hydrogen bonds : angle 4.40092 ( 1260) Misc. bond : bond 0.00039 ( 3) link_TRANS : bond 0.00112 ( 1) link_TRANS : angle 2.07405 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.43 seconds wall clock time: 53 minutes 40.21 seconds (3220.21 seconds total)