Starting phenix.real_space_refine on Wed Sep 17 12:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz4_35833/09_2025/8iz4_35833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz4_35833/09_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_35833/09_2025/8iz4_35833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz4_35833/09_2025/8iz4_35833.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz4_35833/09_2025/8iz4_35833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz4_35833/09_2025/8iz4_35833.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 2, 'GLN:plan1': 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: 2.23, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 343.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.55 Time building geometry restraints manager: 1.17 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- 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 : 4.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (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 ARG 0.002 0.000 ARG R 251 TYR 0.010 0.001 TYR E 190 PHE 0.009 0.001 PHE B 151 TRP 0.009 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9037) covalent geometry : angle 0.38853 (12246) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.70797 ( 6) hydrogen bonds : bond 0.24293 ( 483) hydrogen bonds : angle 7.04319 ( 1365) 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 : 0.347 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 296 TYR cc_start: 0.8067 (t80) cc_final: 0.7793 (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: 0.7834 (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: 0.5488 time to fit residues: 166.1304 Evaluate side-chains 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 E 171 ASN E 179 GLN E 186 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 = 0.3833 r_free = 0.3833 target = 0.155348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104538 restraints weight = 11124.011| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.26 r_work: 0.2990 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2005 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= 0.164 Angle : 0.539 7.357 12252 Z= 0.293 Chirality : 0.043 0.141 1408 Planarity : 0.004 0.043 1534 Dihedral : 6.686 85.537 1329 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.35 % Allowed : 12.91 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1118 helix: 2.84 (0.24), residues: 401 sheet: 0.75 (0.30), residues: 280 loop : 0.11 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 218 TYR 0.015 0.001 TYR R 92 PHE 0.012 0.001 PHE B 241 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9037) covalent geometry : angle 0.53873 (12246) SS BOND : bond 0.00400 ( 3) SS BOND : angle 0.98930 ( 6) hydrogen bonds : bond 0.05322 ( 483) hydrogen bonds : angle 4.73980 ( 1365) Misc. bond : bond 0.00011 ( 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 260 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8779 (mptm) cc_final: 0.8011 (mtmm) REVERT: A 29 LYS cc_start: 0.8340 (tttt) cc_final: 0.7917 (tttp) REVERT: A 208 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7830 (ttp80) REVERT: A 302 TYR cc_start: 0.8616 (t80) cc_final: 0.8324 (t80) REVERT: B 17 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: B 19 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8148 (ttp80) REVERT: B 46 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8086 (mtp85) REVERT: B 59 TYR cc_start: 0.9073 (m-80) cc_final: 0.8503 (m-80) REVERT: B 130 GLU cc_start: 0.8974 (mp0) cc_final: 0.8768 (mp0) REVERT: B 172 GLU cc_start: 0.7987 (tp30) cc_final: 0.7617 (tp30) REVERT: B 215 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 301 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8610 (mtpt) REVERT: C 21 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7279 (ptm) REVERT: C 58 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7996 (mp0) REVERT: E 23 SER cc_start: 0.8510 (m) cc_final: 0.8257 (t) REVERT: E 46 GLU cc_start: 0.8603 (tt0) cc_final: 0.8137 (tm-30) REVERT: E 78 THR cc_start: 0.8121 (m) cc_final: 0.7820 (p) REVERT: E 85 SER cc_start: 0.8799 (m) cc_final: 0.8359 (t) REVERT: R 69 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8503 (tm) outliers start: 51 outliers final: 24 residues processed: 237 average time/residue: 0.5715 time to fit residues: 144.6646 Evaluate side-chains 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 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 R residue 58 THR Chi-restraints excluded: chain R residue 69 LEU 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 1 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105797 restraints weight = 11097.557| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.25 r_work: 0.2971 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9041 Z= 0.137 Angle : 0.506 7.116 12252 Z= 0.274 Chirality : 0.041 0.136 1408 Planarity : 0.003 0.043 1534 Dihedral : 5.941 84.193 1324 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.46 % Allowed : 15.53 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.25), residues: 1118 helix: 2.95 (0.24), residues: 402 sheet: 0.56 (0.29), residues: 285 loop : 0.17 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 218 TYR 0.015 0.001 TYR R 113 PHE 0.012 0.001 PHE R 328 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9037) covalent geometry : angle 0.50537 (12246) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.77403 ( 6) hydrogen bonds : bond 0.04435 ( 483) hydrogen bonds : angle 4.44300 ( 1365) Misc. bond : bond 0.00015 ( 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 260 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8753 (mptm) cc_final: 0.7999 (mtmm) REVERT: A 29 LYS cc_start: 0.8346 (tttt) cc_final: 0.7938 (tttp) REVERT: A 186 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 198 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8792 (ttm) REVERT: A 208 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7845 (ttp80) REVERT: A 273 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7885 (mp) REVERT: A 296 TYR cc_start: 0.8434 (t80) cc_final: 0.7976 (t80) REVERT: A 302 TYR cc_start: 0.8683 (t80) cc_final: 0.8333 (t80) REVERT: A 354 PHE cc_start: 0.8492 (t80) cc_final: 0.8255 (t80) REVERT: B 19 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8198 (ttp80) REVERT: B 46 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.8069 (mtp85) REVERT: B 130 GLU cc_start: 0.8911 (mp0) cc_final: 0.8547 (mp0) REVERT: B 172 GLU cc_start: 0.8045 (tp30) cc_final: 0.7744 (tp30) REVERT: C 21 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7423 (ptm) REVERT: C 58 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7965 (mp0) REVERT: E 23 SER cc_start: 0.8512 (m) cc_final: 0.8235 (t) REVERT: E 46 GLU cc_start: 0.8643 (tt0) cc_final: 0.8162 (tm-30) REVERT: E 85 SER cc_start: 0.8803 (m) cc_final: 0.8327 (t) REVERT: R 177 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7762 (pt) REVERT: R 206 HIS cc_start: 0.8228 (p-80) cc_final: 0.7809 (p-80) REVERT: R 300 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7920 (p90) outliers start: 52 outliers final: 22 residues processed: 231 average time/residue: 0.5917 time to fit residues: 145.7858 Evaluate side-chains 219 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 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 E residue 215 THR Chi-restraints excluded: chain R residue 58 THR 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 300 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 113 GLN 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 = 0.3802 r_free = 0.3802 target = 0.152694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102280 restraints weight = 11285.883| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.25 r_work: 0.2933 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9041 Z= 0.218 Angle : 0.561 8.139 12252 Z= 0.302 Chirality : 0.044 0.157 1408 Planarity : 0.004 0.045 1534 Dihedral : 6.158 89.796 1324 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.77 % Allowed : 17.10 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.25), residues: 1118 helix: 2.74 (0.24), residues: 403 sheet: 0.26 (0.29), residues: 279 loop : 0.13 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.016 0.002 TYR R 92 PHE 0.013 0.002 PHE B 151 TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9037) covalent geometry : angle 0.56071 (12246) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.16621 ( 6) hydrogen bonds : bond 0.04464 ( 483) hydrogen bonds : angle 4.46431 ( 1365) Misc. bond : bond 0.00006 ( 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 245 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8764 (mptm) cc_final: 0.7985 (mtmm) REVERT: A 24 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7276 (mtm110) REVERT: A 29 LYS cc_start: 0.8383 (tttt) cc_final: 0.7899 (tttp) REVERT: A 198 MET cc_start: 0.9088 (ttp) cc_final: 0.8864 (ttm) REVERT: A 208 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7937 (ttp80) REVERT: A 273 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 302 TYR cc_start: 0.8718 (t80) cc_final: 0.8422 (t80) REVERT: A 354 PHE cc_start: 0.8520 (t80) cc_final: 0.8267 (t80) REVERT: B 19 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8158 (ttp80) REVERT: B 46 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8062 (mtp85) REVERT: B 130 GLU cc_start: 0.8881 (mp0) cc_final: 0.8643 (mp0) REVERT: B 172 GLU cc_start: 0.8073 (tp30) cc_final: 0.7781 (tp30) REVERT: B 212 ASP cc_start: 0.8240 (t0) cc_final: 0.7860 (OUTLIER) REVERT: B 215 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7868 (mp0) REVERT: B 217 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7110 (pp-130) REVERT: B 264 TYR cc_start: 0.9155 (m-80) cc_final: 0.8919 (m-80) REVERT: C 21 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7475 (ptm) REVERT: C 58 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7981 (mp0) REVERT: E 23 SER cc_start: 0.8494 (m) cc_final: 0.8214 (t) REVERT: E 46 GLU cc_start: 0.8658 (tt0) cc_final: 0.8202 (tt0) REVERT: E 85 SER cc_start: 0.8847 (m) cc_final: 0.8352 (t) REVERT: R 111 ILE cc_start: 0.8002 (pp) cc_final: 0.7644 (tp) REVERT: R 206 HIS cc_start: 0.8180 (p-80) cc_final: 0.7912 (p-80) REVERT: R 280 VAL cc_start: 0.8636 (t) cc_final: 0.8364 (t) outliers start: 55 outliers final: 31 residues processed: 216 average time/residue: 0.5967 time to fit residues: 137.3483 Evaluate side-chains 217 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET 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 21 MET 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 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 150 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 167 THR 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 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 75 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 = 0.3827 r_free = 0.3827 target = 0.155015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105373 restraints weight = 11210.809| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.21 r_work: 0.2953 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9041 Z= 0.129 Angle : 0.499 6.805 12252 Z= 0.270 Chirality : 0.041 0.136 1408 Planarity : 0.003 0.043 1534 Dihedral : 5.796 89.477 1322 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.88 % Allowed : 19.52 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.25), residues: 1118 helix: 2.83 (0.24), residues: 403 sheet: 0.29 (0.30), residues: 284 loop : 0.20 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.022 0.001 TYR B 59 PHE 0.011 0.001 PHE R 328 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9037) covalent geometry : angle 0.49821 (12246) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.01041 ( 6) hydrogen bonds : bond 0.03950 ( 483) hydrogen bonds : angle 4.29214 ( 1365) Misc. bond : bond 0.00017 ( 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 240 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8756 (mptm) cc_final: 0.7980 (mtmm) REVERT: A 24 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7248 (mtm110) REVERT: A 29 LYS cc_start: 0.8283 (tttt) cc_final: 0.7820 (tttp) REVERT: A 186 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 198 MET cc_start: 0.9041 (ttp) cc_final: 0.8779 (ttm) REVERT: A 208 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7830 (ttp80) REVERT: A 296 TYR cc_start: 0.8498 (t80) cc_final: 0.8268 (t80) REVERT: A 302 TYR cc_start: 0.8698 (t80) cc_final: 0.8432 (t80) REVERT: A 354 PHE cc_start: 0.8517 (t80) cc_final: 0.8290 (t80) REVERT: B 19 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8065 (ttp80) REVERT: B 46 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8084 (mtp85) REVERT: B 130 GLU cc_start: 0.8897 (mp0) cc_final: 0.8547 (mp0) REVERT: B 172 GLU cc_start: 0.8031 (tp30) cc_final: 0.7762 (tp30) REVERT: B 212 ASP cc_start: 0.8115 (t0) cc_final: 0.7721 (OUTLIER) REVERT: B 215 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7833 (mp0) REVERT: B 264 TYR cc_start: 0.9114 (m-80) cc_final: 0.8891 (m-80) REVERT: C 21 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7599 (ptm) REVERT: C 58 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7992 (mp0) REVERT: C 59 ASN cc_start: 0.8690 (t0) cc_final: 0.8318 (t0) REVERT: E 23 SER cc_start: 0.8480 (m) cc_final: 0.8207 (t) REVERT: E 46 GLU cc_start: 0.8638 (tt0) cc_final: 0.8045 (tt0) REVERT: E 85 SER cc_start: 0.8818 (m) cc_final: 0.8332 (t) REVERT: R 111 ILE cc_start: 0.7974 (pp) cc_final: 0.7619 (tp) REVERT: R 150 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8554 (tm) REVERT: R 280 VAL cc_start: 0.8606 (t) cc_final: 0.8337 (t) outliers start: 37 outliers final: 23 residues processed: 223 average time/residue: 0.5613 time to fit residues: 133.8540 Evaluate side-chains 211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 38 ASP 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 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 150 LEU Chi-restraints excluded: chain R residue 154 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 220 GLN E 186 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102244 restraints weight = 11270.192| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.22 r_work: 0.2906 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9041 Z= 0.243 Angle : 0.576 7.228 12252 Z= 0.309 Chirality : 0.045 0.227 1408 Planarity : 0.004 0.045 1534 Dihedral : 5.871 81.946 1322 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.14 % Allowed : 18.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.25), residues: 1118 helix: 2.64 (0.24), residues: 403 sheet: 0.12 (0.30), residues: 276 loop : 0.10 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.014 0.002 TYR R 92 PHE 0.015 0.002 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 9037) covalent geometry : angle 0.57575 (12246) SS BOND : bond 0.00385 ( 3) SS BOND : angle 1.05637 ( 6) hydrogen bonds : bond 0.04378 ( 483) hydrogen bonds : angle 4.45968 ( 1365) Misc. bond : bond 0.00008 ( 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 235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.388 Fit side-chains REVERT: A 17 LYS cc_start: 0.8751 (mptm) cc_final: 0.7995 (mtmm) REVERT: A 24 ARG cc_start: 0.7632 (ttp-110) cc_final: 0.7251 (mtm110) REVERT: A 29 LYS cc_start: 0.8324 (tttt) cc_final: 0.7878 (tttp) REVERT: A 186 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 198 MET cc_start: 0.9095 (ttp) cc_final: 0.8864 (ttm) REVERT: A 208 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7938 (ttp80) REVERT: A 296 TYR cc_start: 0.8350 (t80) cc_final: 0.8146 (t80) REVERT: A 302 TYR cc_start: 0.8739 (t80) cc_final: 0.8436 (t80) REVERT: A 354 PHE cc_start: 0.8561 (t80) cc_final: 0.8303 (t80) REVERT: B 19 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8111 (ttp80) REVERT: B 130 GLU cc_start: 0.8846 (mp0) cc_final: 0.8510 (mp0) REVERT: B 172 GLU cc_start: 0.8091 (tp30) cc_final: 0.7805 (tp30) REVERT: B 212 ASP cc_start: 0.8212 (t0) cc_final: 0.7976 (t0) REVERT: B 300 LEU cc_start: 0.8927 (mt) cc_final: 0.8698 (mt) REVERT: B 336 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 21 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7757 (ptm) REVERT: C 58 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8007 (mp0) REVERT: E 23 SER cc_start: 0.8494 (m) cc_final: 0.8239 (t) REVERT: E 46 GLU cc_start: 0.8674 (tt0) cc_final: 0.8093 (tt0) REVERT: E 62 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: E 85 SER cc_start: 0.8865 (m) cc_final: 0.8345 (t) REVERT: R 111 ILE cc_start: 0.8093 (pp) cc_final: 0.7704 (tp) REVERT: R 280 VAL cc_start: 0.8618 (t) cc_final: 0.8333 (t) outliers start: 49 outliers final: 30 residues processed: 214 average time/residue: 0.6078 time to fit residues: 138.4138 Evaluate side-chains 217 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 38 ASP 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 B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 62 ASP 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 124 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 178 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 331 ASN 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 = 0.3831 r_free = 0.3831 target = 0.155557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106003 restraints weight = 11209.879| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.22 r_work: 0.3038 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9041 Z= 0.118 Angle : 0.511 6.542 12252 Z= 0.274 Chirality : 0.041 0.187 1408 Planarity : 0.003 0.043 1534 Dihedral : 5.665 82.278 1322 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.99 % Allowed : 19.94 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.26), residues: 1118 helix: 2.82 (0.25), residues: 402 sheet: 0.19 (0.30), residues: 276 loop : 0.16 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.014 0.001 TYR E 190 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9037) covalent geometry : angle 0.51085 (12246) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.89638 ( 6) hydrogen bonds : bond 0.03748 ( 483) hydrogen bonds : angle 4.22913 ( 1365) Misc. bond : bond 0.00022 ( 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: 38 poor density : 198 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8829 (mptm) cc_final: 0.8072 (mtmm) REVERT: A 24 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7300 (mtm110) REVERT: A 29 LYS cc_start: 0.8306 (tttt) cc_final: 0.7861 (tttp) REVERT: A 198 MET cc_start: 0.9027 (ttp) cc_final: 0.8778 (ttm) REVERT: A 208 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7886 (ttp80) REVERT: A 302 TYR cc_start: 0.8766 (t80) cc_final: 0.8484 (t80) REVERT: A 354 PHE cc_start: 0.8574 (t80) cc_final: 0.8327 (t80) REVERT: B 46 ARG cc_start: 0.8423 (mtp-110) cc_final: 0.7619 (mmt-90) REVERT: B 130 GLU cc_start: 0.8895 (mp0) cc_final: 0.8644 (mp0) REVERT: B 172 GLU cc_start: 0.8058 (tp30) cc_final: 0.7800 (tp30) REVERT: B 264 TYR cc_start: 0.9034 (m-80) cc_final: 0.8832 (m-80) REVERT: C 58 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8003 (mp0) REVERT: E 23 SER cc_start: 0.8491 (m) cc_final: 0.8272 (t) REVERT: E 46 GLU cc_start: 0.8678 (tt0) cc_final: 0.8124 (tt0) REVERT: E 85 SER cc_start: 0.8838 (m) cc_final: 0.8376 (t) REVERT: R 111 ILE cc_start: 0.8120 (pp) cc_final: 0.7711 (tp) REVERT: R 206 HIS cc_start: 0.8152 (p-80) cc_final: 0.7874 (p-80) REVERT: R 330 MET cc_start: 0.8250 (mmm) cc_final: 0.7859 (mmm) outliers start: 38 outliers final: 22 residues processed: 219 average time/residue: 0.5826 time to fit residues: 136.0343 Evaluate side-chains 211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 154 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 277 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.858 > 50: distance: 13 - 17: 27.942 distance: 17 - 18: 31.390 distance: 18 - 19: 35.781 distance: 18 - 21: 34.996 distance: 19 - 20: 30.577 distance: 19 - 26: 48.019 distance: 21 - 22: 32.574 distance: 23 - 25: 8.217 distance: 26 - 27: 3.484 distance: 26 - 114: 31.237 distance: 27 - 28: 18.200 distance: 27 - 30: 19.132 distance: 28 - 29: 31.061 distance: 28 - 33: 16.753 distance: 29 - 127: 33.846 distance: 33 - 34: 27.034 distance: 34 - 35: 7.315 distance: 34 - 37: 8.093 distance: 35 - 36: 23.208 distance: 35 - 42: 10.305 distance: 38 - 39: 5.258 distance: 39 - 40: 38.892 distance: 40 - 41: 30.961 distance: 42 - 43: 16.052 distance: 42 - 130: 29.223 distance: 43 - 44: 16.108 distance: 43 - 46: 11.799 distance: 44 - 45: 18.439 distance: 44 - 50: 3.440 distance: 45 - 144: 26.138 distance: 46 - 47: 9.918 distance: 47 - 48: 40.753 distance: 47 - 49: 27.360 distance: 50 - 51: 5.444 distance: 50 - 188: 23.596 distance: 51 - 52: 22.820 distance: 51 - 54: 19.980 distance: 52 - 53: 25.822 distance: 52 - 58: 23.957 distance: 53 - 198: 33.915 distance: 54 - 55: 12.999 distance: 55 - 56: 28.472 distance: 55 - 57: 23.120 distance: 58 - 59: 20.368 distance: 58 - 147: 18.946 distance: 59 - 60: 25.823 distance: 59 - 62: 32.659 distance: 60 - 61: 19.205 distance: 60 - 66: 22.256 distance: 62 - 63: 9.940 distance: 63 - 64: 25.178 distance: 63 - 65: 8.137 distance: 66 - 67: 29.493 distance: 66 - 201: 29.888 distance: 67 - 68: 19.905 distance: 67 - 70: 40.240 distance: 68 - 69: 23.788 distance: 68 - 74: 13.069 distance: 69 - 217: 23.610 distance: 70 - 71: 31.328 distance: 71 - 72: 36.918 distance: 71 - 73: 29.675 distance: 74 - 75: 30.751 distance: 76 - 78: 11.034 distance: 79 - 80: 7.859 distance: 79 - 82: 5.068 distance: 80 - 81: 29.109 distance: 80 - 83: 6.971 distance: 83 - 84: 33.241 distance: 84 - 85: 22.570 distance: 85 - 86: 44.232 distance: 85 - 87: 20.012