Starting phenix.real_space_refine on Thu Jan 16 04:54:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgo_38329/01_2025/8xgo_38329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgo_38329/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgo_38329/01_2025/8xgo_38329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgo_38329/01_2025/8xgo_38329.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgo_38329/01_2025/8xgo_38329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgo_38329/01_2025/8xgo_38329.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'NMM:plan-2': 1, 'XZA:plan-1': 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: 5.58, per 1000 atoms: 0.62 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: 2.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 5 " Input volumes are d-peptide like pdb=" CB UYA F 3 " pdb=" CB PHE F 6 " 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: 1.06 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: 2.66 Time building geometry restraints manager: 2.95 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- 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 : 0.007 0.179 9242 Z= 0.452 Angle : 0.678 15.370 12534 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 : 9.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP D 193 HIS 0.003 0.001 HIS B 62 PHE 0.010 0.001 PHE C 61 TYR 0.019 0.001 TYR A 313 ARG 0.003 0.000 ARG B 256 *********************** 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 : 0.962 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: 0.7868 (m-80) outliers start: 2 outliers final: 1 residues processed: 184 average time/residue: 1.5189 time to fit residues: 295.0283 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 : 0.990 ------------------------------------------------------------------------------- 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 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.0070 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 = 0.091379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067123 restraints weight = 17011.546| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.91 r_work: 0.2755 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9242 Z= 0.245 Angle : 0.652 11.005 12534 Z= 0.329 Chirality : 0.045 0.412 1412 Planarity : 0.005 0.046 1593 Dihedral : 5.463 61.560 1274 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.07 % Allowed : 11.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1133 helix: 1.65 (0.27), residues: 400 sheet: -0.52 (0.31), residues: 268 loop : -1.10 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE F 6 TYR 0.031 0.001 TYR A 313 ARG 0.007 0.001 ARG B 22 *********************** 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 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.223 Fit side-chains REVERT: B 217 MET cc_start: 0.7724 (ptm) cc_final: 0.7123 (pp-130) REVERT: C 21 MET cc_start: 0.8710 (tmm) cc_final: 0.8167 (tmm) REVERT: D 28 LEU cc_start: 0.9171 (tt) cc_final: 0.8893 (tm) REVERT: D 99 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8458 (tp40) REVERT: D 240 ASP cc_start: 0.8538 (m-30) cc_final: 0.8137 (m-30) REVERT: E 43 GLU cc_start: 0.8497 (pt0) cc_final: 0.7808 (pp20) REVERT: E 231 GLN cc_start: 0.8793 (mm110) cc_final: 0.8203 (mm110) REVERT: E 259 GLN cc_start: 0.9107 (mm110) cc_final: 0.8874 (mm110) REVERT: E 327 ASP cc_start: 0.8460 (t0) cc_final: 0.8155 (t0) outliers start: 20 outliers final: 6 residues processed: 164 average time/residue: 1.4010 time to fit residues: 243.8920 Evaluate side-chains 150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.089152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064760 restraints weight = 17247.183| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.92 r_work: 0.2703 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9242 Z= 0.347 Angle : 0.660 10.105 12534 Z= 0.335 Chirality : 0.046 0.361 1412 Planarity : 0.005 0.042 1593 Dihedral : 5.637 69.833 1274 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.27 % Allowed : 15.81 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1133 helix: 1.70 (0.27), residues: 395 sheet: -0.53 (0.31), residues: 268 loop : -1.14 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.001 PHE A 48 TYR 0.026 0.002 TYR A 103 ARG 0.006 0.001 ARG B 19 *********************** 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 171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.993 Fit side-chains REVERT: A 54 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8941 (mm) REVERT: B 19 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8438 (ttp-110) REVERT: B 44 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8429 (mm-40) REVERT: B 217 MET cc_start: 0.8009 (ptm) cc_final: 0.7586 (ppp) REVERT: C 21 MET cc_start: 0.8703 (tmm) cc_final: 0.8252 (tmm) REVERT: C 36 ASP cc_start: 0.8717 (m-30) cc_final: 0.8485 (m-30) REVERT: D 28 LEU cc_start: 0.9144 (tt) cc_final: 0.8856 (tm) REVERT: D 240 ASP cc_start: 0.8508 (m-30) cc_final: 0.8148 (m-30) REVERT: E 43 GLU cc_start: 0.8464 (pt0) cc_final: 0.7809 (pp20) REVERT: E 231 GLN cc_start: 0.8798 (mm110) cc_final: 0.8110 (mm110) REVERT: E 327 ASP cc_start: 0.8544 (t0) cc_final: 0.8255 (t0) outliers start: 22 outliers final: 9 residues processed: 156 average time/residue: 1.4074 time to fit residues: 232.7324 Evaluate side-chains 147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.092390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.067110 restraints weight = 16708.415| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.99 r_work: 0.2746 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9242 Z= 0.188 Angle : 0.613 9.436 12534 Z= 0.308 Chirality : 0.043 0.329 1412 Planarity : 0.004 0.039 1593 Dihedral : 5.365 69.329 1274 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.48 % Allowed : 16.84 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1133 helix: 1.89 (0.27), residues: 391 sheet: -0.53 (0.31), residues: 268 loop : -1.13 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.000 HIS A 181 PHE 0.018 0.001 PHE A 48 TYR 0.017 0.001 TYR A 313 ARG 0.007 0.000 ARG C 27 *********************** 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 178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.032 Fit side-chains REVERT: A 54 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8926 (mm) REVERT: B 19 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8450 (ttp-110) REVERT: B 44 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8296 (mm-40) REVERT: B 217 MET cc_start: 0.8011 (ptm) cc_final: 0.7599 (ppp) REVERT: C 21 MET cc_start: 0.8698 (tmm) cc_final: 0.8222 (tmm) REVERT: C 36 ASP cc_start: 0.8680 (m-30) cc_final: 0.8410 (m-30) REVERT: C 47 GLU cc_start: 0.8529 (mp0) cc_final: 0.8319 (mp0) REVERT: D 28 LEU cc_start: 0.9115 (tt) cc_final: 0.8823 (tm) REVERT: D 240 ASP cc_start: 0.8480 (m-30) cc_final: 0.8218 (m-30) REVERT: E 43 GLU cc_start: 0.8457 (pt0) cc_final: 0.7786 (pp20) REVERT: E 231 GLN cc_start: 0.8758 (mm110) cc_final: 0.8080 (mm110) REVERT: E 306 MET cc_start: 0.9051 (ttp) cc_final: 0.8844 (ttm) REVERT: E 327 ASP cc_start: 0.8437 (t0) cc_final: 0.8125 (t0) outliers start: 24 outliers final: 9 residues processed: 164 average time/residue: 1.3739 time to fit residues: 239.1326 Evaluate side-chains 154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 226 GLU Chi-restraints excluded: chain B residue 276 VAL 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 37 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 80 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.091190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.066760 restraints weight = 17059.288| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.92 r_work: 0.2747 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9242 Z= 0.234 Angle : 0.621 9.363 12534 Z= 0.314 Chirality : 0.044 0.324 1412 Planarity : 0.004 0.039 1593 Dihedral : 5.295 68.741 1274 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.79 % Allowed : 18.39 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1133 helix: 1.92 (0.27), residues: 392 sheet: -0.44 (0.32), residues: 266 loop : -1.14 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS A 70 PHE 0.018 0.001 PHE A 48 TYR 0.016 0.001 TYR A 103 ARG 0.007 0.000 ARG C 27 *********************** 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 179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.101 Fit side-chains REVERT: A 54 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8947 (mm) REVERT: B 19 ARG cc_start: 0.8905 (ttp-110) cc_final: 0.8485 (ttp-110) REVERT: B 32 GLN cc_start: 0.8613 (pm20) cc_final: 0.8354 (pm20) REVERT: B 44 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8355 (mm-40) REVERT: B 217 MET cc_start: 0.8096 (ptm) cc_final: 0.7753 (ppp) REVERT: C 21 MET cc_start: 0.8725 (tmm) cc_final: 0.8375 (tmm) REVERT: C 36 ASP cc_start: 0.8741 (m-30) cc_final: 0.8439 (m-30) REVERT: C 47 GLU cc_start: 0.8523 (mp0) cc_final: 0.8261 (mp0) REVERT: D 36 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8909 (tppp) REVERT: D 100 MET cc_start: 0.9252 (mtm) cc_final: 0.9002 (mtm) REVERT: E 43 GLU cc_start: 0.8422 (pt0) cc_final: 0.7759 (pp20) REVERT: E 231 GLN cc_start: 0.8761 (mm110) cc_final: 0.8102 (mm110) REVERT: E 327 ASP cc_start: 0.8487 (t0) cc_final: 0.8173 (t0) outliers start: 27 outliers final: 17 residues processed: 164 average time/residue: 1.4043 time to fit residues: 244.4580 Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 164 THR 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 D residue 264 LEU 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 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.090413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.066016 restraints weight = 16906.059| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.90 r_work: 0.2732 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9242 Z= 0.278 Angle : 0.641 9.759 12534 Z= 0.323 Chirality : 0.044 0.322 1412 Planarity : 0.004 0.041 1593 Dihedral : 5.346 68.624 1274 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.89 % Allowed : 18.60 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1133 helix: 1.88 (0.27), residues: 392 sheet: -0.47 (0.32), residues: 268 loop : -1.10 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.001 PHE A 48 TYR 0.015 0.001 TYR A 103 ARG 0.006 0.000 ARG C 27 *********************** 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: 28 poor density : 150 time to evaluate : 1.028 Fit side-chains REVERT: A 54 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8970 (mm) REVERT: B 19 ARG cc_start: 0.8922 (ttp-110) cc_final: 0.8505 (ttp-110) REVERT: B 32 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: B 44 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8382 (mm-40) REVERT: B 217 MET cc_start: 0.8161 (ptm) cc_final: 0.7853 (ppp) REVERT: C 21 MET cc_start: 0.8730 (tmm) cc_final: 0.8353 (tmm) REVERT: C 36 ASP cc_start: 0.8760 (m-30) cc_final: 0.8455 (m-30) REVERT: C 47 GLU cc_start: 0.8553 (mp0) cc_final: 0.8289 (mp0) REVERT: D 28 LEU cc_start: 0.9093 (tt) cc_final: 0.8827 (tm) REVERT: E 43 GLU cc_start: 0.8403 (pt0) cc_final: 0.7761 (pp20) REVERT: E 231 GLN cc_start: 0.8746 (mm110) cc_final: 0.8100 (mm110) REVERT: E 275 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8658 (mm-30) REVERT: E 327 ASP cc_start: 0.8503 (t0) cc_final: 0.8198 (t0) outliers start: 28 outliers final: 15 residues processed: 163 average time/residue: 1.3767 time to fit residues: 238.2719 Evaluate side-chains 158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.091129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.066815 restraints weight = 17211.395| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.91 r_work: 0.2745 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9242 Z= 0.234 Angle : 0.636 9.414 12534 Z= 0.320 Chirality : 0.044 0.315 1412 Planarity : 0.004 0.043 1593 Dihedral : 5.232 67.802 1274 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.79 % Allowed : 19.52 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1133 helix: 1.93 (0.27), residues: 392 sheet: -0.41 (0.32), residues: 266 loop : -1.11 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS A 70 PHE 0.024 0.001 PHE A 48 TYR 0.014 0.001 TYR D 207 ARG 0.007 0.000 ARG C 27 *********************** 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 179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8971 (mm) REVERT: A 70 HIS cc_start: 0.8707 (t70) cc_final: 0.8475 (t-90) REVERT: B 19 ARG cc_start: 0.8928 (ttp-110) cc_final: 0.8511 (ttp-110) REVERT: B 32 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: B 44 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8396 (mm-40) REVERT: B 217 MET cc_start: 0.8172 (ptm) cc_final: 0.7865 (ppp) REVERT: C 21 MET cc_start: 0.8746 (tmm) cc_final: 0.8363 (tmm) REVERT: C 36 ASP cc_start: 0.8749 (m-30) cc_final: 0.8461 (m-30) REVERT: C 47 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: D 28 LEU cc_start: 0.9068 (tt) cc_final: 0.8792 (tm) REVERT: E 43 GLU cc_start: 0.8424 (pt0) cc_final: 0.7819 (pp20) REVERT: E 204 ARG cc_start: 0.8413 (mmp80) cc_final: 0.7913 (mmp80) REVERT: E 231 GLN cc_start: 0.8753 (mm110) cc_final: 0.8141 (mm110) REVERT: E 275 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8656 (mm-30) REVERT: E 289 TYR cc_start: 0.8705 (t80) cc_final: 0.8324 (t80) REVERT: E 327 ASP cc_start: 0.8487 (t0) cc_final: 0.8172 (t0) outliers start: 27 outliers final: 16 residues processed: 165 average time/residue: 1.3709 time to fit residues: 240.2504 Evaluate side-chains 166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 33 ILE Chi-restraints excluded: chain B residue 114 CYS 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 47 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 73 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 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 = 0.3351 r_free = 0.3351 target = 0.091739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.067689 restraints weight = 17214.839| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.90 r_work: 0.2763 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9242 Z= 0.211 Angle : 0.634 9.779 12534 Z= 0.319 Chirality : 0.043 0.305 1412 Planarity : 0.004 0.044 1593 Dihedral : 5.116 66.551 1274 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.07 % Allowed : 20.76 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1133 helix: 1.98 (0.27), residues: 392 sheet: -0.31 (0.32), residues: 260 loop : -1.18 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS A 70 PHE 0.022 0.001 PHE A 48 TYR 0.014 0.001 TYR D 207 ARG 0.007 0.000 ARG C 27 *********************** 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 170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.001 Fit side-chains REVERT: B 19 ARG cc_start: 0.8928 (ttp-110) cc_final: 0.8524 (ttp-110) REVERT: B 32 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: B 217 MET cc_start: 0.8203 (ptm) cc_final: 0.7855 (ppp) REVERT: B 259 GLN cc_start: 0.8391 (tt0) cc_final: 0.8097 (tt0) REVERT: C 21 MET cc_start: 0.8761 (tmm) cc_final: 0.8387 (tmm) REVERT: C 36 ASP cc_start: 0.8733 (m-30) cc_final: 0.8434 (m-30) REVERT: C 47 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: D 28 LEU cc_start: 0.9075 (tt) cc_final: 0.8796 (tm) REVERT: D 100 MET cc_start: 0.9314 (mtm) cc_final: 0.9003 (mtp) REVERT: E 43 GLU cc_start: 0.8432 (pt0) cc_final: 0.7820 (pp20) REVERT: E 204 ARG cc_start: 0.8421 (mmp80) cc_final: 0.7890 (mmp80) REVERT: E 231 GLN cc_start: 0.8755 (mm110) cc_final: 0.8172 (mm110) REVERT: E 275 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8749 (mm-30) REVERT: E 289 TYR cc_start: 0.8690 (t80) cc_final: 0.8313 (t80) REVERT: E 327 ASP cc_start: 0.8480 (t0) cc_final: 0.8191 (t0) outliers start: 20 outliers final: 14 residues processed: 160 average time/residue: 1.3834 time to fit residues: 234.8685 Evaluate side-chains 156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 65 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** D 99 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 = 0.3326 r_free = 0.3326 target = 0.090217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.065837 restraints weight = 16954.351| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.90 r_work: 0.2727 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9242 Z= 0.296 Angle : 0.666 10.258 12534 Z= 0.336 Chirality : 0.045 0.322 1412 Planarity : 0.004 0.044 1593 Dihedral : 5.228 66.165 1274 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.07 % Allowed : 21.28 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1133 helix: 1.85 (0.27), residues: 398 sheet: -0.28 (0.32), residues: 256 loop : -1.12 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 70 PHE 0.025 0.001 PHE A 48 TYR 0.013 0.001 TYR D 207 ARG 0.007 0.000 ARG C 27 *********************** 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 171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8942 (ttp-110) cc_final: 0.8540 (ttp-110) REVERT: B 217 MET cc_start: 0.8225 (ptm) cc_final: 0.7866 (ppp) REVERT: C 21 MET cc_start: 0.8733 (tmm) cc_final: 0.8341 (tmm) REVERT: C 36 ASP cc_start: 0.8751 (m-30) cc_final: 0.8443 (m-30) REVERT: C 47 GLU cc_start: 0.8597 (mp0) cc_final: 0.8293 (mp0) REVERT: D 28 LEU cc_start: 0.9092 (tt) cc_final: 0.8820 (tm) REVERT: D 36 LYS cc_start: 0.9132 (tppt) cc_final: 0.8877 (tppp) REVERT: D 99 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8295 (mm-40) REVERT: D 100 MET cc_start: 0.9336 (mtm) cc_final: 0.9022 (mtp) REVERT: D 104 ARG cc_start: 0.8871 (ptp90) cc_final: 0.8612 (ptp90) REVERT: D 235 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7875 (tpm-80) REVERT: E 43 GLU cc_start: 0.8406 (pt0) cc_final: 0.7792 (pp20) REVERT: E 204 ARG cc_start: 0.8423 (mmp80) cc_final: 0.7915 (mmp80) REVERT: E 215 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: E 231 GLN cc_start: 0.8739 (mm110) cc_final: 0.8126 (mm110) REVERT: E 275 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8750 (mm-30) REVERT: E 289 TYR cc_start: 0.8681 (t80) cc_final: 0.8301 (t80) REVERT: E 327 ASP cc_start: 0.8487 (t0) cc_final: 0.8195 (t0) outliers start: 20 outliers final: 13 residues processed: 165 average time/residue: 1.3951 time to fit residues: 244.4236 Evaluate side-chains 155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 270 LEU 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 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 12 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** D 99 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 = 0.3360 r_free = 0.3360 target = 0.092323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.068096 restraints weight = 17112.833| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.92 r_work: 0.2767 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9242 Z= 0.203 Angle : 0.665 10.919 12534 Z= 0.334 Chirality : 0.044 0.309 1412 Planarity : 0.004 0.046 1593 Dihedral : 5.108 64.758 1274 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.76 % Allowed : 21.90 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1133 helix: 1.90 (0.27), residues: 399 sheet: -0.30 (0.32), residues: 264 loop : -1.15 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS A 70 PHE 0.026 0.001 PHE A 48 TYR 0.023 0.001 TYR A 103 ARG 0.008 0.000 ARG C 27 ********************** 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 167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.9388 (m-40) cc_final: 0.9172 (m-40) REVERT: B 19 ARG cc_start: 0.8935 (ttp-110) cc_final: 0.8490 (ttp-110) REVERT: B 32 GLN cc_start: 0.8412 (pm20) cc_final: 0.8143 (pm20) REVERT: B 217 MET cc_start: 0.8232 (ptm) cc_final: 0.7891 (ppp) REVERT: B 259 GLN cc_start: 0.8382 (tt0) cc_final: 0.8094 (tt0) REVERT: C 21 MET cc_start: 0.8708 (tmm) cc_final: 0.8323 (tmm) REVERT: C 36 ASP cc_start: 0.8777 (m-30) cc_final: 0.8478 (m-30) REVERT: C 47 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: D 28 LEU cc_start: 0.9089 (tt) cc_final: 0.8819 (tm) REVERT: D 100 MET cc_start: 0.9338 (mtm) cc_final: 0.9081 (mtp) REVERT: D 235 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7839 (tpm-80) REVERT: E 17 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8444 (mmtp) REVERT: E 43 GLU cc_start: 0.8434 (pt0) cc_final: 0.7808 (pp20) REVERT: E 204 ARG cc_start: 0.8434 (mmp80) cc_final: 0.7908 (mmp80) REVERT: E 215 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8179 (tp30) REVERT: E 231 GLN cc_start: 0.8741 (mm110) cc_final: 0.8166 (mm110) REVERT: E 275 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8743 (mm-30) REVERT: E 289 TYR cc_start: 0.8661 (t80) cc_final: 0.8400 (t80) REVERT: E 327 ASP cc_start: 0.8446 (t0) cc_final: 0.8157 (t0) outliers start: 17 outliers final: 14 residues processed: 160 average time/residue: 1.5059 time to fit residues: 255.6755 Evaluate side-chains 161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU 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 D residue 203 GLN 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 43 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068136 restraints weight = 17009.172| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.91 r_work: 0.2771 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9242 Z= 0.213 Angle : 0.655 10.829 12534 Z= 0.328 Chirality : 0.044 0.313 1412 Planarity : 0.004 0.036 1593 Dihedral : 5.040 63.393 1274 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.76 % Allowed : 22.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1133 helix: 1.95 (0.27), residues: 398 sheet: -0.42 (0.32), residues: 278 loop : -1.10 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 70 PHE 0.026 0.001 PHE A 48 TYR 0.015 0.001 TYR A 103 ARG 0.007 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6516.62 seconds wall clock time: 116 minutes 7.23 seconds (6967.23 seconds total)