Starting phenix.real_space_refine on Mon May 12 04:43:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz4_35833/05_2025/8iz4_35833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz4_35833/05_2025/8iz4_35833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iz4_35833/05_2025/8iz4_35833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz4_35833/05_2025/8iz4_35833.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz4_35833/05_2025/8iz4_35833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz4_35833/05_2025/8iz4_35833.cif" } resolution = 2.93 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= 0.011 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 64 5.16 5 C 5655 2.51 5 N 1486 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8857 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2210 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'TJR': 1} Inner-chain residues flagged as termini: ['pdbres="SER R 602 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.39, per 1000 atoms: 0.61 Number of scatterers: 8857 At special positions: 0 Unit cell: (110.21, 127.33, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 1 15.00 O 1651 8.00 N 1486 7.00 C 5655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 39.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.545A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.020A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.706A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.908A 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 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.576A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 116 Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.564A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 197 removed outlier: 4.077A pdb=" N GLY R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 Processing helix chain 'R' and resid 259 through 295 Proline residue: R 281 - end of helix removed outlier: 3.967A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 331 removed outlier: 3.591A pdb=" N GLU R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL R 314 " --> pdb=" O GLU R 310 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix Processing helix chain 'R' and resid 331 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.738A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.576A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.543A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.972A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.268A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.688A 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: 6.791A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.280A 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: 6.519A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.925A 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: 3.752A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.852A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.288A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.596A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1365 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: 2.53 Time building geometry restraints manager: 2.77 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: 1423 1.31 - 1.43: 2505 1.43 - 1.56: 5015 1.56 - 1.68: 1 1.68 - 1.81: 93 Bond restraints: 9037 Sorted by residual: bond pdb=" CAK TJR R 601 " pdb=" OAJ TJR R 601 " ideal model delta sigma weight residual 1.344 1.398 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" CAI TJR R 601 " pdb=" OAJ TJR R 601 " ideal model delta sigma weight residual 1.446 1.398 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" OAD TJR R 601 " pdb=" PAC TJR R 601 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" OAF TJR R 601 " pdb=" PAC TJR R 601 " ideal model delta sigma weight residual 1.679 1.647 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" CAK TJR R 601 " pdb=" OAE TJR R 601 " ideal model delta sigma weight residual 1.213 1.184 0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 9032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 12159 1.63 - 3.25: 75 3.25 - 4.88: 8 4.88 - 6.51: 3 6.51 - 8.14: 1 Bond angle restraints: 12246 Sorted by residual: angle pdb=" CAI TJR R 601 " pdb=" OAJ TJR R 601 " pdb=" CAK TJR R 601 " ideal model delta sigma weight residual 121.91 113.77 8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" OAD TJR R 601 " pdb=" PAC TJR R 601 " pdb=" OAF TJR R 601 " ideal model delta sigma weight residual 104.39 109.76 -5.37 3.00e+00 1.11e-01 3.20e+00 angle pdb=" CAG TJR R 601 " pdb=" CAH TJR R 601 " pdb=" OBC TJR R 601 " ideal model delta sigma weight residual 112.70 107.86 4.84 3.00e+00 1.11e-01 2.61e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 126.33 -2.40 1.54e+00 4.22e-01 2.43e+00 ... (remaining 12241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5180 16.96 - 33.91: 163 33.91 - 50.87: 37 50.87 - 67.83: 12 67.83 - 84.78: 2 Dihedral angle restraints: 5394 sinusoidal: 2102 harmonic: 3292 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 841 0.026 - 0.051: 337 0.051 - 0.076: 146 0.076 - 0.102: 51 0.102 - 0.127: 33 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 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 2.40 0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1405 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B 236 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 255 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO R 256 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 256 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 256 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO B 194 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.015 5.00e-02 4.00e+02 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1763 2.78 - 3.31: 8318 3.31 - 3.84: 14728 3.84 - 4.37: 18077 4.37 - 4.90: 31569 Nonbonded interactions: 74455 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A 341 " pdb=" OH TYR R 261 " model vdw 2.267 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.279 3.040 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.286 3.120 ... (remaining 74450 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 22.770 Find NCS groups from input model: 0.070 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 0.090 9041 Z= 0.136 Angle : 0.389 8.137 12252 Z= 0.202 Chirality : 0.038 0.127 1408 Planarity : 0.003 0.043 1534 Dihedral : 9.423 84.784 3263 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.15 % Allowed : 3.04 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.08 (0.24), residues: 1118 helix: 1.65 (0.25), residues: 413 sheet: 0.69 (0.29), residues: 281 loop : -0.09 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE B 151 TYR 0.010 0.001 TYR E 190 ARG 0.002 0.000 ARG R 251 Details of bonding type rmsd hydrogen bonds : bond 0.24293 ( 483) hydrogen bonds : angle 7.04319 ( 1365) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.70797 ( 6) covalent geometry : bond 0.00211 ( 9037) covalent geometry : angle 0.38853 (12246) Misc. bond : bond 0.09011 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 276 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8766 (mptm) cc_final: 0.7991 (mtmm) REVERT: A 21 ARG cc_start: 0.8264 (ttm110) cc_final: 0.8021 (ttm110) REVERT: A 186 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7872 (mm-30) REVERT: A 208 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7707 (ttp80) REVERT: A 251 ASP cc_start: 0.7961 (t70) cc_final: 0.7654 (OUTLIER) REVERT: A 302 TYR cc_start: 0.8659 (t80) cc_final: 0.8423 (t80) REVERT: A 331 ASN cc_start: 0.8857 (m-40) cc_final: 0.8531 (m-40) REVERT: B 19 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7995 (ttp80) REVERT: B 46 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7846 (mtp85) REVERT: B 172 GLU cc_start: 0.7598 (tp30) cc_final: 0.7189 (tp30) REVERT: B 212 ASP cc_start: 0.8178 (t0) cc_final: 0.7856 (t0) REVERT: B 219 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7918 (mtp180) REVERT: B 259 GLN cc_start: 0.8659 (pt0) cc_final: 0.7949 (pt0) REVERT: B 301 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8670 (mtpt) REVERT: C 17 GLU cc_start: 0.8560 (tp30) cc_final: 0.8227 (tp30) REVERT: C 58 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7773 (mp0) REVERT: E 18 ARG cc_start: 0.8002 (tpt-90) cc_final: 0.7691 (tpt-90) REVERT: E 23 SER cc_start: 0.8537 (m) cc_final: 0.8300 (t) REVERT: E 43 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8141 (mmmm) REVERT: E 46 GLU cc_start: 0.8152 (tt0) cc_final: 0.7703 (tm-30) REVERT: E 78 THR cc_start: 0.8318 (m) cc_final: 0.8071 (p) REVERT: R 203 MET cc_start: 0.8409 (pmm) cc_final: 0.8142 (pp-130) outliers start: 11 outliers final: 10 residues processed: 283 average time/residue: 1.0130 time to fit residues: 307.7425 Evaluate side-chains 209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 TYR Chi-restraints excluded: chain R residue 602 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 255 ASN B 75 GLN E 171 ASN E 179 GLN R 83 HIS ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106252 restraints weight = 10971.998| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.24 r_work: 0.2995 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9041 Z= 0.139 Angle : 0.527 7.432 12252 Z= 0.285 Chirality : 0.042 0.142 1408 Planarity : 0.004 0.042 1534 Dihedral : 6.704 84.657 1331 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.25 % Allowed : 12.91 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.89 (0.25), residues: 1118 helix: 2.82 (0.24), residues: 403 sheet: 0.79 (0.30), residues: 280 loop : 0.13 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 227 TYR 0.015 0.001 TYR E 190 ARG 0.004 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 483) hydrogen bonds : angle 4.67493 ( 1365) SS BOND : bond 0.00399 ( 3) SS BOND : angle 0.98133 ( 6) covalent geometry : bond 0.00295 ( 9037) covalent geometry : angle 0.52658 (12246) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8760 (mptm) cc_final: 0.7992 (mtmm) REVERT: A 29 LYS cc_start: 0.8328 (tttt) cc_final: 0.7911 (tttp) REVERT: A 208 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7790 (ttp80) REVERT: A 302 TYR cc_start: 0.8586 (t80) cc_final: 0.8304 (t80) REVERT: A 318 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: B 17 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8367 (tp40) REVERT: B 19 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8150 (ttp80) REVERT: B 46 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.8087 (mtp85) REVERT: B 59 TYR cc_start: 0.9068 (m-80) cc_final: 0.8588 (m-80) REVERT: B 130 GLU cc_start: 0.8925 (mp0) cc_final: 0.8718 (mp0) REVERT: B 172 GLU cc_start: 0.7975 (tp30) cc_final: 0.7598 (tp30) REVERT: B 215 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 264 TYR cc_start: 0.9082 (m-80) cc_final: 0.8791 (m-80) REVERT: B 301 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8604 (mtpt) REVERT: C 21 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7284 (ptm) REVERT: C 58 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7991 (mp0) REVERT: E 23 SER cc_start: 0.8499 (m) cc_final: 0.8245 (t) REVERT: E 46 GLU cc_start: 0.8586 (tt0) cc_final: 0.8116 (tm-30) REVERT: E 78 THR cc_start: 0.8090 (m) cc_final: 0.7785 (p) REVERT: E 85 SER cc_start: 0.8754 (m) cc_final: 0.8353 (t) REVERT: R 69 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8521 (tm) REVERT: R 73 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8824 (pp) REVERT: R 111 ILE cc_start: 0.7904 (pp) cc_final: 0.7530 (tp) REVERT: R 304 ILE cc_start: 0.8590 (tp) cc_final: 0.8322 (tp) REVERT: R 308 THR cc_start: 0.8894 (m) cc_final: 0.8660 (p) outliers start: 50 outliers final: 23 residues processed: 235 average time/residue: 1.0089 time to fit residues: 254.5617 Evaluate side-chains 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 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 269 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104842 restraints weight = 11158.738| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.26 r_work: 0.2977 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9041 Z= 0.157 Angle : 0.518 7.454 12252 Z= 0.280 Chirality : 0.042 0.136 1408 Planarity : 0.003 0.043 1534 Dihedral : 6.170 84.239 1324 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.98 % Allowed : 14.80 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.91 (0.25), residues: 1118 helix: 3.01 (0.24), residues: 403 sheet: 0.51 (0.29), residues: 284 loop : 0.16 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 114 PHE 0.011 0.001 PHE B 151 TYR 0.015 0.001 TYR R 92 ARG 0.002 0.000 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 483) hydrogen bonds : angle 4.46039 ( 1365) SS BOND : bond 0.00326 ( 3) SS BOND : angle 0.84372 ( 6) covalent geometry : bond 0.00356 ( 9037) covalent geometry : angle 0.51779 (12246) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8762 (mptm) cc_final: 0.8002 (mtmm) REVERT: A 29 LYS cc_start: 0.8351 (tttt) cc_final: 0.7958 (tttp) REVERT: A 208 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7859 (ttp80) REVERT: A 273 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 296 TYR cc_start: 0.8624 (t80) cc_final: 0.8319 (t80) REVERT: A 302 TYR cc_start: 0.8681 (t80) cc_final: 0.8329 (t80) REVERT: A 354 PHE cc_start: 0.8463 (t80) cc_final: 0.8224 (t80) REVERT: B 19 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8178 (ttp80) REVERT: B 46 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.8064 (mtp85) REVERT: B 130 GLU cc_start: 0.8916 (mp0) cc_final: 0.8554 (mp0) REVERT: B 172 GLU cc_start: 0.8055 (tp30) cc_final: 0.7755 (tp30) REVERT: B 212 ASP cc_start: 0.8250 (t0) cc_final: 0.8014 (t0) REVERT: B 215 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 21 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7433 (ptm) REVERT: C 58 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7973 (mp0) REVERT: E 23 SER cc_start: 0.8491 (m) cc_final: 0.8224 (t) REVERT: E 46 GLU cc_start: 0.8638 (tt0) cc_final: 0.8162 (tm-30) REVERT: E 78 THR cc_start: 0.8072 (m) cc_final: 0.7741 (p) REVERT: E 85 SER cc_start: 0.8806 (m) cc_final: 0.8338 (t) REVERT: R 69 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8733 (tm) REVERT: R 206 HIS cc_start: 0.8176 (p-80) cc_final: 0.7761 (p-80) REVERT: R 300 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7951 (p90) outliers start: 57 outliers final: 29 residues processed: 233 average time/residue: 1.0864 time to fit residues: 271.1172 Evaluate side-chains 228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107100 restraints weight = 11001.693| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.23 r_work: 0.3008 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9041 Z= 0.117 Angle : 0.486 8.245 12252 Z= 0.262 Chirality : 0.041 0.143 1408 Planarity : 0.003 0.043 1534 Dihedral : 5.988 84.019 1324 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.51 % Allowed : 18.15 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.86 (0.25), residues: 1118 helix: 2.91 (0.24), residues: 403 sheet: 0.50 (0.30), residues: 281 loop : 0.18 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.011 0.001 PHE R 186 TYR 0.014 0.001 TYR R 92 ARG 0.004 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 483) hydrogen bonds : angle 4.25835 ( 1365) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.04078 ( 6) covalent geometry : bond 0.00257 ( 9037) covalent geometry : angle 0.48517 (12246) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8753 (mptm) cc_final: 0.7992 (mtmm) REVERT: A 29 LYS cc_start: 0.8278 (tttt) cc_final: 0.7795 (tttp) REVERT: A 32 ARG cc_start: 0.7295 (mtm110) cc_final: 0.7034 (mtm110) REVERT: A 198 MET cc_start: 0.9011 (ttp) cc_final: 0.8718 (ttm) REVERT: A 208 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7782 (ttp80) REVERT: A 273 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 302 TYR cc_start: 0.8674 (t80) cc_final: 0.8346 (t80) REVERT: A 318 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7437 (pt0) REVERT: A 354 PHE cc_start: 0.8493 (t80) cc_final: 0.8252 (t80) REVERT: B 19 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8209 (ttp80) REVERT: B 42 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7794 (tpt-90) REVERT: B 46 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.8060 (mtp85) REVERT: B 130 GLU cc_start: 0.8896 (mp0) cc_final: 0.8564 (mp0) REVERT: B 172 GLU cc_start: 0.8034 (tp30) cc_final: 0.7757 (tp30) REVERT: B 212 ASP cc_start: 0.8179 (t0) cc_final: 0.7891 (t0) REVERT: B 259 GLN cc_start: 0.8909 (pt0) cc_final: 0.8350 (pt0) REVERT: B 264 TYR cc_start: 0.9104 (m-80) cc_final: 0.8845 (m-80) REVERT: C 21 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7467 (ptm) REVERT: C 58 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7977 (mp0) REVERT: E 23 SER cc_start: 0.8482 (m) cc_final: 0.8211 (t) REVERT: E 46 GLU cc_start: 0.8614 (tt0) cc_final: 0.8158 (tm-30) REVERT: E 85 SER cc_start: 0.8808 (m) cc_final: 0.8341 (t) REVERT: R 111 ILE cc_start: 0.7976 (pp) cc_final: 0.7639 (tp) REVERT: R 177 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (pt) REVERT: R 206 HIS cc_start: 0.8177 (p-80) cc_final: 0.7896 (p-80) REVERT: R 280 VAL cc_start: 0.8647 (t) cc_final: 0.8385 (t) outliers start: 43 outliers final: 23 residues processed: 221 average time/residue: 1.0944 time to fit residues: 258.5960 Evaluate side-chains 216 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 326 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 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 52 GLN A 255 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107655 restraints weight = 11110.000| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.22 r_work: 0.3103 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9041 Z= 0.108 Angle : 0.480 7.599 12252 Z= 0.256 Chirality : 0.041 0.132 1408 Planarity : 0.003 0.042 1534 Dihedral : 5.646 86.128 1322 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.09 % Allowed : 19.20 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.87 (0.25), residues: 1118 helix: 2.96 (0.24), residues: 404 sheet: 0.48 (0.30), residues: 274 loop : 0.16 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 114 PHE 0.010 0.001 PHE R 186 TYR 0.012 0.001 TYR E 190 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 483) hydrogen bonds : angle 4.16147 ( 1365) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.91862 ( 6) covalent geometry : bond 0.00233 ( 9037) covalent geometry : angle 0.47975 (12246) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8769 (mptm) cc_final: 0.8006 (mtmm) REVERT: A 29 LYS cc_start: 0.8266 (tttt) cc_final: 0.7769 (tttp) REVERT: A 32 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6957 (mtm110) REVERT: A 198 MET cc_start: 0.8951 (ttp) cc_final: 0.8664 (ttm) REVERT: A 208 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7752 (ttp80) REVERT: A 273 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 296 TYR cc_start: 0.8556 (t80) cc_final: 0.8345 (t80) REVERT: A 302 TYR cc_start: 0.8705 (t80) cc_final: 0.8451 (t80) REVERT: A 354 PHE cc_start: 0.8477 (t80) cc_final: 0.8269 (t80) REVERT: B 19 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8084 (ttp80) REVERT: B 46 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.7993 (mtp85) REVERT: B 130 GLU cc_start: 0.8897 (mp0) cc_final: 0.8651 (mp0) REVERT: B 172 GLU cc_start: 0.8041 (tp30) cc_final: 0.7657 (tp30) REVERT: B 212 ASP cc_start: 0.8060 (t0) cc_final: 0.7829 (t0) REVERT: B 259 GLN cc_start: 0.8938 (pt0) cc_final: 0.8371 (pt0) REVERT: C 21 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7593 (ptm) REVERT: C 58 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7990 (mp0) REVERT: E 23 SER cc_start: 0.8484 (m) cc_final: 0.8225 (t) REVERT: E 46 GLU cc_start: 0.8605 (tt0) cc_final: 0.8120 (tm-30) REVERT: E 85 SER cc_start: 0.8801 (m) cc_final: 0.8341 (t) REVERT: R 111 ILE cc_start: 0.7978 (pp) cc_final: 0.7617 (tp) REVERT: R 280 VAL cc_start: 0.8658 (t) cc_final: 0.8410 (t) REVERT: R 308 THR cc_start: 0.8640 (p) cc_final: 0.8438 (t) outliers start: 39 outliers final: 23 residues processed: 222 average time/residue: 1.0089 time to fit residues: 240.4620 Evaluate side-chains 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 326 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107715 restraints weight = 11092.187| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.21 r_work: 0.3085 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9041 Z= 0.112 Angle : 0.489 7.367 12252 Z= 0.260 Chirality : 0.041 0.213 1408 Planarity : 0.003 0.041 1534 Dihedral : 5.527 86.576 1322 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.78 % Allowed : 19.83 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.87 (0.25), residues: 1118 helix: 2.93 (0.25), residues: 404 sheet: 0.50 (0.30), residues: 280 loop : 0.18 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.039 0.001 PHE R 219 TYR 0.012 0.001 TYR E 190 ARG 0.004 0.000 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 483) hydrogen bonds : angle 4.11517 ( 1365) SS BOND : bond 0.00332 ( 3) SS BOND : angle 0.79765 ( 6) covalent geometry : bond 0.00245 ( 9037) covalent geometry : angle 0.48846 (12246) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.957 Fit side-chains REVERT: A 17 LYS cc_start: 0.8772 (mptm) cc_final: 0.8008 (mtmm) REVERT: A 24 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7213 (mtm110) REVERT: A 29 LYS cc_start: 0.8285 (tttt) cc_final: 0.7791 (tttp) REVERT: A 198 MET cc_start: 0.8929 (ttp) cc_final: 0.8681 (ttm) REVERT: A 208 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7749 (ttp80) REVERT: A 302 TYR cc_start: 0.8746 (t80) cc_final: 0.8498 (t80) REVERT: A 354 PHE cc_start: 0.8499 (t80) cc_final: 0.8279 (t80) REVERT: B 42 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7764 (tpt-90) REVERT: B 46 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7856 (mtp85) REVERT: B 130 GLU cc_start: 0.8885 (mp0) cc_final: 0.8619 (mp0) REVERT: B 172 GLU cc_start: 0.8042 (tp30) cc_final: 0.7657 (tp30) REVERT: B 212 ASP cc_start: 0.8054 (t0) cc_final: 0.7799 (t0) REVERT: B 215 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8120 (mm-30) REVERT: B 264 TYR cc_start: 0.9011 (m-80) cc_final: 0.8757 (m-80) REVERT: C 58 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7991 (mp0) REVERT: E 23 SER cc_start: 0.8538 (m) cc_final: 0.8302 (t) REVERT: E 46 GLU cc_start: 0.8616 (tt0) cc_final: 0.8156 (tt0) REVERT: E 85 SER cc_start: 0.8803 (m) cc_final: 0.8335 (t) REVERT: R 111 ILE cc_start: 0.8014 (pp) cc_final: 0.7626 (tp) REVERT: R 206 HIS cc_start: 0.8051 (p-80) cc_final: 0.7694 (p-80) REVERT: R 280 VAL cc_start: 0.8640 (t) cc_final: 0.8393 (t) outliers start: 36 outliers final: 21 residues processed: 214 average time/residue: 1.1215 time to fit residues: 257.5174 Evaluate side-chains 210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 326 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105072 restraints weight = 11228.481| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.22 r_work: 0.2960 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9041 Z= 0.159 Angle : 0.541 7.639 12252 Z= 0.286 Chirality : 0.042 0.162 1408 Planarity : 0.003 0.042 1534 Dihedral : 5.609 88.825 1322 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.62 % Allowed : 19.62 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.68 (0.25), residues: 1118 helix: 2.75 (0.25), residues: 402 sheet: 0.41 (0.30), residues: 281 loop : 0.11 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE R 219 TYR 0.015 0.001 TYR A 296 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 483) hydrogen bonds : angle 4.26935 ( 1365) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.86492 ( 6) covalent geometry : bond 0.00367 ( 9037) covalent geometry : angle 0.54049 (12246) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 1.013 Fit side-chains REVERT: A 17 LYS cc_start: 0.8732 (mptm) cc_final: 0.7961 (mtmm) REVERT: A 24 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7222 (mtm110) REVERT: A 29 LYS cc_start: 0.8266 (tttt) cc_final: 0.7776 (tttp) REVERT: A 198 MET cc_start: 0.8960 (ttp) cc_final: 0.8662 (ttm) REVERT: A 208 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7738 (ttp80) REVERT: A 302 TYR cc_start: 0.8709 (t80) cc_final: 0.8433 (t80) REVERT: A 354 PHE cc_start: 0.8557 (t80) cc_final: 0.8302 (t80) REVERT: B 42 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7865 (tpt-90) REVERT: B 46 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7997 (mtp85) REVERT: B 75 GLN cc_start: 0.8329 (mt0) cc_final: 0.8038 (mt0) REVERT: B 130 GLU cc_start: 0.8870 (mp0) cc_final: 0.8586 (mp0) REVERT: B 172 GLU cc_start: 0.8063 (tp30) cc_final: 0.7655 (tp30) REVERT: B 212 ASP cc_start: 0.8092 (t0) cc_final: 0.7744 (t0) REVERT: B 264 TYR cc_start: 0.9068 (m-80) cc_final: 0.8792 (m-80) REVERT: B 300 LEU cc_start: 0.8970 (mt) cc_final: 0.8737 (mt) REVERT: C 58 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8018 (mp0) REVERT: E 23 SER cc_start: 0.8533 (m) cc_final: 0.8292 (t) REVERT: E 62 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: E 85 SER cc_start: 0.8816 (m) cc_final: 0.8281 (t) REVERT: R 206 HIS cc_start: 0.8079 (p-80) cc_final: 0.7731 (p-80) REVERT: R 280 VAL cc_start: 0.8601 (t) cc_final: 0.8357 (t) outliers start: 44 outliers final: 25 residues processed: 217 average time/residue: 1.0933 time to fit residues: 254.3476 Evaluate side-chains 215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 326 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 84 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 44 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.154819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104829 restraints weight = 11275.749| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.22 r_work: 0.2930 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9041 Z= 0.160 Angle : 0.541 7.893 12252 Z= 0.288 Chirality : 0.042 0.163 1408 Planarity : 0.003 0.042 1534 Dihedral : 5.738 89.654 1322 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.78 % Allowed : 21.30 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.70 (0.25), residues: 1118 helix: 2.76 (0.25), residues: 403 sheet: 0.40 (0.30), residues: 281 loop : 0.13 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.024 0.001 TYR A 296 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 483) hydrogen bonds : angle 4.26870 ( 1365) SS BOND : bond 0.00334 ( 3) SS BOND : angle 0.84512 ( 6) covalent geometry : bond 0.00373 ( 9037) covalent geometry : angle 0.54071 (12246) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.979 Fit side-chains REVERT: A 17 LYS cc_start: 0.8727 (mptm) cc_final: 0.7948 (mtmm) REVERT: A 24 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7225 (mtm110) REVERT: A 29 LYS cc_start: 0.8203 (tttt) cc_final: 0.7769 (tttp) REVERT: A 198 MET cc_start: 0.8950 (ttp) cc_final: 0.8688 (ttm) REVERT: A 208 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7789 (ttp80) REVERT: A 302 TYR cc_start: 0.8700 (t80) cc_final: 0.8421 (t80) REVERT: A 354 PHE cc_start: 0.8577 (t80) cc_final: 0.8319 (t80) REVERT: B 42 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7870 (tpt-90) REVERT: B 46 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7991 (mtp85) REVERT: B 130 GLU cc_start: 0.8849 (mp0) cc_final: 0.8563 (mp0) REVERT: B 172 GLU cc_start: 0.8067 (tp30) cc_final: 0.7755 (tp30) REVERT: B 212 ASP cc_start: 0.8124 (t0) cc_final: 0.7755 (t0) REVERT: B 264 TYR cc_start: 0.9054 (m-80) cc_final: 0.8832 (m-80) REVERT: C 58 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8007 (mp0) REVERT: E 23 SER cc_start: 0.8456 (m) cc_final: 0.8178 (t) REVERT: E 85 SER cc_start: 0.8825 (m) cc_final: 0.8292 (t) REVERT: R 183 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8110 (mm) REVERT: R 206 HIS cc_start: 0.8060 (p-80) cc_final: 0.7723 (p-80) REVERT: R 330 MET cc_start: 0.8598 (mmm) cc_final: 0.7892 (mmm) outliers start: 36 outliers final: 26 residues processed: 213 average time/residue: 1.1237 time to fit residues: 255.9427 Evaluate side-chains 214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107204 restraints weight = 11233.110| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.22 r_work: 0.2950 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9041 Z= 0.123 Angle : 0.536 8.342 12252 Z= 0.281 Chirality : 0.041 0.172 1408 Planarity : 0.003 0.041 1534 Dihedral : 5.524 89.998 1320 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.83 % Allowed : 22.46 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.74 (0.26), residues: 1118 helix: 2.79 (0.25), residues: 403 sheet: 0.44 (0.30), residues: 282 loop : 0.14 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE B 151 TYR 0.022 0.001 TYR A 296 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 483) hydrogen bonds : angle 4.18711 ( 1365) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.72541 ( 6) covalent geometry : bond 0.00275 ( 9037) covalent geometry : angle 0.53571 (12246) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.032 Fit side-chains REVERT: A 17 LYS cc_start: 0.8709 (mptm) cc_final: 0.7937 (mtmm) REVERT: A 24 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7227 (mtm110) REVERT: A 29 LYS cc_start: 0.8184 (tttt) cc_final: 0.7750 (tttp) REVERT: A 198 MET cc_start: 0.8887 (ttp) cc_final: 0.8649 (ttm) REVERT: A 208 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7716 (ttp80) REVERT: A 302 TYR cc_start: 0.8740 (t80) cc_final: 0.8483 (t80) REVERT: A 354 PHE cc_start: 0.8576 (t80) cc_final: 0.8310 (t80) REVERT: B 42 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7861 (tpt-90) REVERT: B 46 ARG cc_start: 0.8310 (mtp-110) cc_final: 0.7990 (mtp85) REVERT: B 130 GLU cc_start: 0.8840 (mp0) cc_final: 0.8537 (mp0) REVERT: B 172 GLU cc_start: 0.8030 (tp30) cc_final: 0.7644 (tp30) REVERT: B 212 ASP cc_start: 0.7988 (t0) cc_final: 0.7671 (t0) REVERT: B 264 TYR cc_start: 0.9043 (m-80) cc_final: 0.8808 (m-80) REVERT: C 58 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7993 (mp0) REVERT: E 17 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8980 (p) REVERT: E 23 SER cc_start: 0.8414 (m) cc_final: 0.8172 (t) REVERT: E 85 SER cc_start: 0.8852 (m) cc_final: 0.8329 (t) REVERT: R 183 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (mm) REVERT: R 186 PHE cc_start: 0.7568 (t80) cc_final: 0.7250 (t80) REVERT: R 206 HIS cc_start: 0.8063 (p-80) cc_final: 0.7797 (p-80) REVERT: R 330 MET cc_start: 0.8461 (mmm) cc_final: 0.7853 (mmm) outliers start: 27 outliers final: 18 residues processed: 213 average time/residue: 1.1113 time to fit residues: 253.5143 Evaluate side-chains 214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 85 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105465 restraints weight = 11237.002| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.21 r_work: 0.2928 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9041 Z= 0.161 Angle : 0.552 8.168 12252 Z= 0.292 Chirality : 0.042 0.183 1408 Planarity : 0.003 0.042 1534 Dihedral : 5.559 86.655 1319 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.41 % Allowed : 22.98 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.63 (0.25), residues: 1118 helix: 2.62 (0.25), residues: 410 sheet: 0.37 (0.31), residues: 276 loop : 0.13 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 114 PHE 0.012 0.001 PHE B 151 TYR 0.025 0.001 TYR A 296 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 483) hydrogen bonds : angle 4.23261 ( 1365) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.78554 ( 6) covalent geometry : bond 0.00374 ( 9037) covalent geometry : angle 0.55144 (12246) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.933 Fit side-chains REVERT: A 17 LYS cc_start: 0.8726 (mptm) cc_final: 0.7956 (mtmm) REVERT: A 24 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7242 (mtm110) REVERT: A 29 LYS cc_start: 0.8220 (tttt) cc_final: 0.7784 (tttp) REVERT: A 198 MET cc_start: 0.8917 (ttp) cc_final: 0.8675 (ttm) REVERT: A 208 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7846 (ttp80) REVERT: A 302 TYR cc_start: 0.8729 (t80) cc_final: 0.8463 (t80) REVERT: A 354 PHE cc_start: 0.8592 (t80) cc_final: 0.8339 (t80) REVERT: B 19 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7863 (ttp80) REVERT: B 42 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7881 (tpt-90) REVERT: B 130 GLU cc_start: 0.8860 (mp0) cc_final: 0.8576 (mp0) REVERT: B 172 GLU cc_start: 0.8046 (tp30) cc_final: 0.7730 (tp30) REVERT: B 212 ASP cc_start: 0.8081 (t0) cc_final: 0.7727 (t0) REVERT: B 264 TYR cc_start: 0.9073 (m-80) cc_final: 0.8755 (m-80) REVERT: C 58 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7996 (mp0) REVERT: E 23 SER cc_start: 0.8489 (m) cc_final: 0.8264 (t) REVERT: E 62 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: E 85 SER cc_start: 0.8819 (m) cc_final: 0.8263 (t) REVERT: R 183 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8105 (mm) REVERT: R 206 HIS cc_start: 0.8102 (p-80) cc_final: 0.7770 (p-80) REVERT: R 330 MET cc_start: 0.8509 (mmm) cc_final: 0.7910 (mmm) outliers start: 23 outliers final: 19 residues processed: 209 average time/residue: 1.1191 time to fit residues: 249.9838 Evaluate side-chains 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104490 restraints weight = 11241.782| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.20 r_work: 0.2987 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9041 Z= 0.188 Angle : 0.575 8.391 12252 Z= 0.303 Chirality : 0.043 0.178 1408 Planarity : 0.004 0.042 1534 Dihedral : 5.529 82.226 1319 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.83 % Allowed : 22.98 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.56 (0.25), residues: 1118 helix: 2.56 (0.25), residues: 410 sheet: 0.33 (0.31), residues: 276 loop : 0.10 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 114 PHE 0.012 0.001 PHE B 151 TYR 0.027 0.001 TYR A 296 ARG 0.009 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 483) hydrogen bonds : angle 4.28901 ( 1365) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.96459 ( 6) covalent geometry : bond 0.00442 ( 9037) covalent geometry : angle 0.57509 (12246) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8530.23 seconds wall clock time: 147 minutes 15.41 seconds (8835.41 seconds total)