Starting phenix.real_space_refine on Fri Dec 27 22:05:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk8_33247/12_2024/7xk8_33247.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk8_33247/12_2024/7xk8_33247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk8_33247/12_2024/7xk8_33247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk8_33247/12_2024/7xk8_33247.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk8_33247/12_2024/7xk8_33247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk8_33247/12_2024/7xk8_33247.cif" } resolution = 3.3 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= -0.000 sd= 0.003 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 46 5.16 5 C 4352 2.51 5 N 1151 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6796 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 202 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2115 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 99 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1673 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2432 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 373 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.63, per 1000 atoms: 0.68 Number of scatterers: 6796 At special positions: 0 Unit cell: (111.815, 127.49, 85.69, 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 46 16.00 O 1247 8.00 N 1151 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 43.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'R' and resid 45 through 72 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 78 through 108 Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 150 through 156 Processing helix chain 'R' and resid 157 through 159 No H-bonds generated for 'chain 'R' and resid 157 through 159' Processing helix chain 'R' and resid 160 through 184 Proline residue: R 180 - end of helix Processing helix chain 'R' and resid 209 through 247 removed outlier: 4.502A pdb=" N LEU R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) Proline residue: R 228 - end of helix Processing helix chain 'R' and resid 259 through 282 Processing helix chain 'R' and resid 282 through 292 removed outlier: 3.987A pdb=" N ARG R 288 " --> pdb=" O PHE R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 328 Proline residue: R 324 - end of helix Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.993A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.624A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.172A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.264A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'C' and resid 12 through 21 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.747A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 197 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 36 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.224A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.832A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.863A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.271A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.988A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.672A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.140A 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: 3.802A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1068 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: 1.72 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1099 1.31 - 1.44: 1926 1.44 - 1.56: 3855 1.56 - 1.69: 0 1.69 - 1.82: 62 Bond restraints: 6942 Sorted by residual: bond pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.10e-02 2.27e+03 3.46e+01 bond pdb=" CG ASN P 25 " pdb=" OD1 ASN P 25 " ideal model delta sigma weight residual 1.231 1.185 0.046 1.90e-02 2.77e+03 5.92e+00 bond pdb=" C ASN P 25 " pdb=" O ASN P 25 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C SER P 9 " pdb=" N PRO P 10 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 bond pdb=" N PRO R 193 " pdb=" CA PRO R 193 " ideal model delta sigma weight residual 1.469 1.475 -0.006 7.40e-03 1.83e+04 7.36e-01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 9231 1.23 - 2.46: 184 2.46 - 3.68: 41 3.68 - 4.91: 11 4.91 - 6.14: 8 Bond angle restraints: 9475 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 112.96 109.56 3.40 1.00e+00 1.00e+00 1.16e+01 angle pdb=" N GLY R 186 " pdb=" CA GLY R 186 " pdb=" C GLY R 186 " ideal model delta sigma weight residual 110.80 115.68 -4.88 1.71e+00 3.42e-01 8.15e+00 angle pdb=" OD1 ASN P 25 " pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 122.60 119.99 2.61 1.00e+00 1.00e+00 6.82e+00 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 113.65 110.02 3.63 1.47e+00 4.63e-01 6.11e+00 angle pdb=" CB ASN P 25 " pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 116.40 120.02 -3.62 1.50e+00 4.44e-01 5.81e+00 ... (remaining 9470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 3698 15.57 - 31.14: 291 31.14 - 46.70: 57 46.70 - 62.27: 7 62.27 - 77.84: 1 Dihedral angle restraints: 4054 sinusoidal: 1361 harmonic: 2693 Sorted by residual: dihedral pdb=" CA PHE R 189 " pdb=" C PHE R 189 " pdb=" N HIS R 190 " pdb=" CA HIS R 190 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 65.34 27.66 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " pdb=" CG ASP B 38 " pdb=" OD1 ASP B 38 " ideal model delta sinusoidal sigma weight residual -30.00 -83.44 53.44 1 2.00e+01 2.50e-03 9.71e+00 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 756 0.030 - 0.059: 243 0.059 - 0.089: 79 0.089 - 0.119: 44 0.119 - 0.149: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE R 187 " pdb=" N ILE R 187 " pdb=" C ILE R 187 " pdb=" CB ILE R 187 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB ILE R 184 " pdb=" CA ILE R 184 " pdb=" CG1 ILE R 184 " pdb=" CG2 ILE R 184 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1122 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 78 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO R 79 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 79 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 79 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 282 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 283 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.20e-01 pdb=" N PRO B 236 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.013 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1396 2.78 - 3.31: 6603 3.31 - 3.84: 11498 3.84 - 4.37: 12427 4.37 - 4.90: 22105 Nonbonded interactions: 54029 Sorted by model distance: nonbonded pdb=" O LEU R 289 " pdb=" OG SER R 292 " model vdw 2.248 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR R 78 " pdb=" OD1 ASP A 350 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.278 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.306 3.040 ... (remaining 54024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 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 : 0.002 0.124 6942 Z= 0.142 Angle : 0.479 6.142 9475 Z= 0.271 Chirality : 0.038 0.149 1125 Planarity : 0.003 0.029 1203 Dihedral : 11.624 77.838 2301 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.25 (0.25), residues: 907 helix: 0.38 (0.24), residues: 371 sheet: -0.45 (0.38), residues: 154 loop : -2.23 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 99 HIS 0.003 0.000 HIS R 285 PHE 0.010 0.001 PHE R 291 TYR 0.004 0.001 TYR B 289 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 127 GLU cc_start: 0.6422 (tp30) cc_final: 0.6077 (tp30) REVERT: R 333 ARG cc_start: 0.4321 (pmt170) cc_final: 0.3932 (tpp-160) REVERT: A 9 ASP cc_start: 0.7360 (t70) cc_final: 0.6993 (t0) REVERT: B 188 MET cc_start: 0.7046 (mmm) cc_final: 0.6843 (mmm) REVERT: C 62 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6392 (mtm110) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2204 time to fit residues: 45.3237 Evaluate side-chains 99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.0870 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 43 HIS R 285 HIS A 57 HIS A 294 ASN A 304 GLN A 347 ASN B 340 ASN C 18 GLN C 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6942 Z= 0.235 Angle : 0.592 7.509 9475 Z= 0.305 Chirality : 0.042 0.237 1125 Planarity : 0.003 0.028 1203 Dihedral : 3.657 29.105 978 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.24 % Allowed : 14.93 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.17 (0.27), residues: 907 helix: 1.56 (0.26), residues: 373 sheet: -0.41 (0.39), residues: 145 loop : -1.72 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.023 0.002 PHE R 316 TYR 0.019 0.002 TYR R 213 ARG 0.005 0.001 ARG R 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: R 104 TYR cc_start: 0.4285 (m-80) cc_final: 0.3814 (m-80) REVERT: R 333 ARG cc_start: 0.4523 (pmt170) cc_final: 0.3875 (tpp-160) REVERT: A 9 ASP cc_start: 0.7444 (t70) cc_final: 0.7082 (t0) REVERT: A 52 GLN cc_start: 0.6754 (pp30) cc_final: 0.6106 (pp30) REVERT: C 62 ARG cc_start: 0.6738 (mtm-85) cc_final: 0.6439 (mtm110) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.2115 time to fit residues: 36.0586 Evaluate side-chains 109 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6942 Z= 0.194 Angle : 0.554 6.525 9475 Z= 0.285 Chirality : 0.041 0.178 1125 Planarity : 0.003 0.030 1203 Dihedral : 3.736 34.595 978 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.28 % Allowed : 17.91 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.25 (0.27), residues: 907 helix: 1.91 (0.27), residues: 376 sheet: -0.27 (0.41), residues: 139 loop : -1.45 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 285 PHE 0.017 0.001 PHE R 316 TYR 0.017 0.001 TYR R 213 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: R 104 TYR cc_start: 0.4484 (m-80) cc_final: 0.3998 (m-80) REVERT: R 281 TRP cc_start: 0.5026 (m100) cc_final: 0.4441 (m100) REVERT: R 333 ARG cc_start: 0.4278 (pmt170) cc_final: 0.3781 (tpp-160) REVERT: A 9 ASP cc_start: 0.7440 (t70) cc_final: 0.7060 (t0) REVERT: A 247 MET cc_start: 0.7038 (ptp) cc_final: 0.6796 (mtm) REVERT: C 62 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6507 (mtm110) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.1836 time to fit residues: 31.1484 Evaluate side-chains 116 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 82 optimal weight: 0.0050 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 0.0000 chunk 49 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6942 Z= 0.167 Angle : 0.546 6.898 9475 Z= 0.277 Chirality : 0.041 0.158 1125 Planarity : 0.003 0.029 1203 Dihedral : 3.718 35.637 978 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.88 % Allowed : 19.25 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.46 (0.28), residues: 907 helix: 2.11 (0.27), residues: 376 sheet: -0.34 (0.42), residues: 141 loop : -1.29 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 285 PHE 0.018 0.001 PHE R 316 TYR 0.012 0.001 TYR R 213 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.780 Fit side-chains REVERT: R 49 SER cc_start: 0.5700 (t) cc_final: 0.4895 (p) REVERT: R 104 TYR cc_start: 0.4470 (m-80) cc_final: 0.3976 (m-80) REVERT: R 210 MET cc_start: 0.4143 (tpp) cc_final: 0.3721 (tpp) REVERT: R 281 TRP cc_start: 0.5032 (m100) cc_final: 0.4537 (m100) REVERT: R 333 ARG cc_start: 0.4534 (pmt170) cc_final: 0.3910 (tpp-160) REVERT: A 9 ASP cc_start: 0.7413 (t70) cc_final: 0.7044 (t0) REVERT: A 197 LYS cc_start: 0.8044 (ptpt) cc_final: 0.7817 (ptmt) REVERT: C 62 ARG cc_start: 0.6783 (mtm-85) cc_final: 0.6528 (mtm110) outliers start: 26 outliers final: 16 residues processed: 127 average time/residue: 0.1799 time to fit residues: 31.0184 Evaluate side-chains 115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6942 Z= 0.400 Angle : 0.677 10.119 9475 Z= 0.346 Chirality : 0.045 0.164 1125 Planarity : 0.004 0.036 1203 Dihedral : 4.402 43.094 978 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.07 % Allowed : 20.15 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.28), residues: 907 helix: 1.98 (0.26), residues: 376 sheet: -0.76 (0.39), residues: 165 loop : -1.40 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.006 0.002 HIS A 188 PHE 0.019 0.002 PHE R 316 TYR 0.022 0.002 TYR B 59 ARG 0.004 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.592 Fit side-chains REVERT: R 169 ILE cc_start: 0.4817 (OUTLIER) cc_final: 0.4429 (tp) REVERT: R 239 MET cc_start: 0.6020 (mtp) cc_final: 0.5577 (ttm) REVERT: R 333 ARG cc_start: 0.4341 (pmt170) cc_final: 0.3621 (tmt170) outliers start: 34 outliers final: 19 residues processed: 130 average time/residue: 0.1952 time to fit residues: 34.8193 Evaluate side-chains 117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6942 Z= 0.207 Angle : 0.588 9.017 9475 Z= 0.297 Chirality : 0.042 0.276 1125 Planarity : 0.003 0.033 1203 Dihedral : 4.135 41.436 978 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.18 % Allowed : 22.24 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.34 (0.28), residues: 907 helix: 2.14 (0.27), residues: 375 sheet: -0.74 (0.40), residues: 154 loop : -1.36 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.752 Fit side-chains REVERT: R 49 SER cc_start: 0.5839 (t) cc_final: 0.5070 (p) REVERT: R 210 MET cc_start: 0.4253 (tpp) cc_final: 0.3801 (tpp) REVERT: R 239 MET cc_start: 0.5780 (mtp) cc_final: 0.5413 (ttm) REVERT: R 333 ARG cc_start: 0.4243 (pmt170) cc_final: 0.3592 (tmt170) outliers start: 28 outliers final: 20 residues processed: 130 average time/residue: 0.1758 time to fit residues: 31.0798 Evaluate side-chains 115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.0470 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6942 Z= 0.204 Angle : 0.587 8.961 9475 Z= 0.296 Chirality : 0.042 0.265 1125 Planarity : 0.003 0.032 1203 Dihedral : 4.042 39.779 978 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.48 % Allowed : 23.88 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.36 (0.28), residues: 907 helix: 2.20 (0.26), residues: 375 sheet: -0.90 (0.40), residues: 149 loop : -1.31 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE R 316 TYR 0.018 0.001 TYR B 59 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.640 Fit side-chains REVERT: R 49 SER cc_start: 0.5862 (t) cc_final: 0.5084 (p) REVERT: R 210 MET cc_start: 0.4275 (tpp) cc_final: 0.3840 (tpp) REVERT: R 239 MET cc_start: 0.5687 (mtp) cc_final: 0.5371 (ttm) REVERT: R 333 ARG cc_start: 0.4243 (pmt170) cc_final: 0.3603 (tmt170) outliers start: 30 outliers final: 25 residues processed: 121 average time/residue: 0.1635 time to fit residues: 27.3891 Evaluate side-chains 121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 16 optimal weight: 0.0770 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6942 Z= 0.177 Angle : 0.582 9.658 9475 Z= 0.292 Chirality : 0.042 0.263 1125 Planarity : 0.003 0.032 1203 Dihedral : 3.905 38.373 978 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.33 % Allowed : 24.33 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.47 (0.27), residues: 907 helix: 2.25 (0.26), residues: 376 sheet: -0.82 (0.42), residues: 138 loop : -1.23 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE R 316 TYR 0.019 0.001 TYR B 59 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.769 Fit side-chains REVERT: R 49 SER cc_start: 0.5857 (t) cc_final: 0.5090 (p) REVERT: R 84 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5987 (mp) REVERT: R 210 MET cc_start: 0.4538 (tpp) cc_final: 0.4164 (tpp) REVERT: R 333 ARG cc_start: 0.4309 (pmt170) cc_final: 0.3693 (tmt170) outliers start: 29 outliers final: 26 residues processed: 120 average time/residue: 0.1782 time to fit residues: 29.4230 Evaluate side-chains 121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6942 Z= 0.178 Angle : 0.579 8.589 9475 Z= 0.291 Chirality : 0.042 0.262 1125 Planarity : 0.003 0.031 1203 Dihedral : 3.865 37.106 978 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.78 % Allowed : 24.18 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.52 (0.28), residues: 907 helix: 2.25 (0.26), residues: 377 sheet: -0.71 (0.40), residues: 154 loop : -1.21 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 285 PHE 0.031 0.001 PHE R 316 TYR 0.020 0.001 TYR B 59 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: R 49 SER cc_start: 0.5672 (t) cc_final: 0.4932 (p) REVERT: R 84 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5892 (mp) REVERT: R 210 MET cc_start: 0.4403 (tpp) cc_final: 0.3808 (tpp) REVERT: R 333 ARG cc_start: 0.4295 (pmt170) cc_final: 0.3687 (tmt170) REVERT: A 197 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7965 (ptmt) REVERT: B 82 TRP cc_start: 0.7631 (m100) cc_final: 0.7126 (m100) outliers start: 32 outliers final: 26 residues processed: 119 average time/residue: 0.1770 time to fit residues: 29.7980 Evaluate side-chains 127 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 7 optimal weight: 0.0030 chunk 55 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6942 Z= 0.167 Angle : 0.583 9.244 9475 Z= 0.294 Chirality : 0.042 0.261 1125 Planarity : 0.003 0.032 1203 Dihedral : 3.790 35.604 978 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.88 % Allowed : 25.67 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.53 (0.28), residues: 907 helix: 2.24 (0.26), residues: 377 sheet: -0.69 (0.40), residues: 160 loop : -1.18 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.030 0.001 PHE R 316 TYR 0.009 0.001 TYR R 225 ARG 0.004 0.000 ARG A 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: R 49 SER cc_start: 0.5585 (t) cc_final: 0.4849 (p) REVERT: R 84 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5907 (mp) REVERT: R 210 MET cc_start: 0.4363 (tpp) cc_final: 0.3802 (tpp) REVERT: R 263 ARG cc_start: 0.4992 (tmm160) cc_final: 0.4354 (tmm160) REVERT: R 333 ARG cc_start: 0.4274 (pmt170) cc_final: 0.3678 (tmt170) REVERT: A 197 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7964 (ptmt) REVERT: B 82 TRP cc_start: 0.7593 (m100) cc_final: 0.7176 (m100) outliers start: 26 outliers final: 21 residues processed: 118 average time/residue: 0.1616 time to fit residues: 26.9696 Evaluate side-chains 121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.207892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.163559 restraints weight = 7452.934| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.21 r_work: 0.3881 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6942 Z= 0.206 Angle : 0.597 10.315 9475 Z= 0.301 Chirality : 0.042 0.260 1125 Planarity : 0.003 0.033 1203 Dihedral : 3.844 36.942 978 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.18 % Allowed : 25.97 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.50 (0.28), residues: 907 helix: 2.23 (0.26), residues: 377 sheet: -0.84 (0.39), residues: 165 loop : -1.14 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.031 0.001 PHE R 316 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.34 seconds wall clock time: 36 minutes 1.79 seconds (2161.79 seconds total)