Starting phenix.real_space_refine on Thu Jul 2 08:28:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1k_13163/07_2026/7p1k_13163_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1k_13163/07_2026/7p1k_13163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p1k_13163/07_2026/7p1k_13163_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1k_13163/07_2026/7p1k_13163_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p1k_13163/07_2026/7p1k_13163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1k_13163/07_2026/7p1k_13163.map" } resolution = 3.64 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= 0.005 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 4 5.49 5 S 38 5.16 5 C 4648 2.51 5 N 1032 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6892 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3243 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3243 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 203 Unusual residues: {'T7X': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-2': 1, 'T7X:plan-3': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 203 Unusual residues: {'T7X': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-2': 1, 'T7X:plan-3': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.32, per 1000 atoms: 0.19 Number of scatterers: 6892 At special positions: 0 Unit cell: (75.0915, 77.121, 118.726, 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 38 16.00 P 4 15.00 O 1170 8.00 N 1032 7.00 C 4648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 289.2 milliseconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 80 through 104 removed outlier: 3.822A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.704A pdb=" N GLY B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.342A pdb=" N GLY B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.811A pdb=" N SER B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 168 through 190 removed outlier: 3.523A pdb=" N ILE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 removed outlier: 3.509A pdb=" N LEU B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 226 removed outlier: 3.709A pdb=" N VAL B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.573A pdb=" N PHE B 234 " --> pdb=" O TRP B 230 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 259 removed outlier: 3.922A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.588A pdb=" N SER B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.665A pdb=" N ALA B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 319 removed outlier: 3.759A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 removed outlier: 3.741A pdb=" N ALA B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 377 removed outlier: 3.869A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 3.608A pdb=" N LYS B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Proline residue: B 397 - end of helix removed outlier: 3.616A pdb=" N PHE B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 439 removed outlier: 3.572A pdb=" N VAL B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 455 removed outlier: 3.796A pdb=" N ILE B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 removed outlier: 4.048A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 480 through 516 removed outlier: 4.179A pdb=" N GLY B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Proline residue: B 502 - end of helix removed outlier: 3.560A pdb=" N GLY B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Proline residue: B 513 - end of helix removed outlier: 3.884A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 104 removed outlier: 3.792A pdb=" N LEU A 96 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 131 removed outlier: 3.543A pdb=" N ILE A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.559A pdb=" N SER A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 168 through 190 removed outlier: 3.527A pdb=" N ILE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 removed outlier: 3.620A pdb=" N LEU A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 226 removed outlier: 3.785A pdb=" N VAL A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.698A pdb=" N MET A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.743A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.566A pdb=" N SER A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.617A pdb=" N ALA A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.691A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.500A pdb=" N ALA A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.026A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.551A pdb=" N VAL A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 397 - end of helix removed outlier: 3.605A pdb=" N PHE A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 460 through 466 removed outlier: 4.056A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 480 through 516 removed outlier: 3.572A pdb=" N TYR A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Proline residue: A 502 - end of helix removed outlier: 3.519A pdb=" N LEU A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Proline residue: A 513 - end of helix removed outlier: 3.854A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1347 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: 1.01 Time building geometry restraints manager: 0.78 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: 1015 1.31 - 1.43: 1725 1.43 - 1.56: 4156 1.56 - 1.68: 104 1.68 - 1.81: 56 Bond restraints: 7056 Sorted by residual: bond pdb=" C21 T7X A 806 " pdb=" C22 T7X A 806 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C21 T7X B1203 " pdb=" C22 T7X B1203 " ideal model delta sigma weight residual 1.329 1.527 -0.198 2.00e-02 2.50e+03 9.83e+01 bond pdb=" C24 T7X A 806 " pdb=" C25 T7X A 806 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.75e+01 bond pdb=" C24 T7X B1203 " pdb=" C25 T7X B1203 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" C15 T7X B1203 " pdb=" C16 T7X B1203 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.62e+01 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 9475 3.75 - 7.50: 131 7.50 - 11.25: 21 11.25 - 15.00: 15 15.00 - 18.75: 4 Bond angle restraints: 9646 Sorted by residual: angle pdb=" O11 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O12 T7X B1203 " ideal model delta sigma weight residual 119.67 100.92 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" O11 T7X A 806 " pdb=" P1 T7X A 806 " pdb=" O12 T7X A 806 " ideal model delta sigma weight residual 119.67 101.10 18.57 3.00e+00 1.11e-01 3.83e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 114.31 106.98 7.33 1.29e+00 6.01e-01 3.23e+01 angle pdb=" O1 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O13 T7X B1203 " ideal model delta sigma weight residual 94.60 110.62 -16.02 3.00e+00 1.11e-01 2.85e+01 angle pdb=" N TRP B 171 " pdb=" CA TRP B 171 " pdb=" C TRP B 171 " ideal model delta sigma weight residual 113.50 107.07 6.43 1.23e+00 6.61e-01 2.73e+01 ... (remaining 9641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 4325 32.78 - 65.56: 103 65.56 - 98.33: 11 98.33 - 131.11: 5 131.11 - 163.89: 2 Dihedral angle restraints: 4446 sinusoidal: 2034 harmonic: 2412 Sorted by residual: dihedral pdb=" C15 T7X A 806 " pdb=" C16 T7X A 806 " pdb=" C17 T7X A 806 " pdb=" C18 T7X A 806 " ideal model delta sinusoidal sigma weight residual 111.73 -84.38 -163.89 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C15 T7X B1203 " pdb=" C16 T7X B1203 " pdb=" C17 T7X B1203 " pdb=" C18 T7X B1203 " ideal model delta sinusoidal sigma weight residual 111.73 -87.94 -160.33 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CAR Y01 B1204 " pdb=" CAV Y01 B1204 " pdb=" CBC Y01 B1204 " pdb=" CAZ Y01 B1204 " ideal model delta sinusoidal sigma weight residual 55.40 -56.96 112.36 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1112 0.074 - 0.148: 59 0.148 - 0.222: 23 0.222 - 0.296: 2 0.296 - 0.370: 8 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CBG Y01 A 804 " pdb=" CAQ Y01 A 804 " pdb=" CBD Y01 A 804 " pdb=" CBI Y01 A 804 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CBG Y01 B1201 " pdb=" CAQ Y01 B1201 " pdb=" CBD Y01 B1201 " pdb=" CBI Y01 B1201 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CBG Y01 A 803 " pdb=" CAQ Y01 A 803 " pdb=" CBD Y01 A 803 " pdb=" CBI Y01 A 803 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1201 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 T7X A 806 " 0.135 2.00e-02 2.50e+03 3.42e-01 1.17e+03 pdb=" C18 T7X A 806 " -0.438 2.00e-02 2.50e+03 pdb=" C19 T7X A 806 " 0.476 2.00e-02 2.50e+03 pdb=" C20 T7X A 806 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 T7X A 806 " 0.150 2.00e-02 2.50e+03 3.31e-01 1.10e+03 pdb=" C24 T7X A 806 " -0.437 2.00e-02 2.50e+03 pdb=" C25 T7X A 806 " 0.447 2.00e-02 2.50e+03 pdb=" C26 T7X A 806 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 T7X B1203 " -0.152 2.00e-02 2.50e+03 3.11e-01 9.67e+02 pdb=" C24 T7X B1203 " 0.410 2.00e-02 2.50e+03 pdb=" C25 T7X B1203 " -0.414 2.00e-02 2.50e+03 pdb=" C26 T7X B1203 " 0.156 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 52 2.60 - 3.17: 6088 3.17 - 3.75: 10006 3.75 - 4.32: 13397 4.32 - 4.90: 22515 Nonbonded interactions: 52058 Sorted by model distance: nonbonded pdb=" N GLU A 385 " pdb=" OE1 GLU A 385 " model vdw 2.023 3.120 nonbonded pdb=" O PHE A 153 " pdb=" ND2 ASN A 157 " model vdw 2.200 3.120 nonbonded pdb=" O PHE B 153 " pdb=" ND2 ASN B 157 " model vdw 2.231 3.120 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.238 3.120 nonbonded pdb=" O VAL B 239 " pdb=" NE2 GLN B 463 " model vdw 2.304 3.120 ... (remaining 52053 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 79 through 801 or resid 804)) selection = (chain 'B' and (resid 79 through 1201 or resid 1204)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.630 Find NCS groups from input model: 0.100 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 : 0.014 0.199 7056 Z= 0.696 Angle : 1.118 18.751 9646 Z= 0.459 Chirality : 0.053 0.370 1204 Planarity : 0.024 0.342 1118 Dihedral : 14.123 163.890 2910 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.61 % Allowed : 7.93 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.19 (0.29), residues: 858 helix: 0.60 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.10 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.005 0.001 TYR A 260 PHE 0.005 0.001 PHE A 300 TRP 0.020 0.001 TRP A 171 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.01377 / 0.70 ( 7056) covalent geometry : angle 1.11845 / 0.46 ( 9646) hydrogen bonds : bond 0.29096 / 18.97 ( 449) hydrogen bonds : angle 6.94714 / 4.96 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.152 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 200 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7014 (mmtt) REVERT: B 226 MET cc_start: 0.6218 (mmt) cc_final: 0.5976 (mpp) REVERT: B 346 SER cc_start: 0.7929 (t) cc_final: 0.7727 (m) REVERT: B 426 ILE cc_start: 0.8581 (mt) cc_final: 0.8376 (mm) REVERT: B 438 MET cc_start: 0.7032 (mmm) cc_final: 0.6743 (mmt) REVERT: B 507 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 86 VAL cc_start: 0.6782 (m) cc_final: 0.6572 (t) REVERT: A 96 LEU cc_start: 0.8447 (tt) cc_final: 0.8125 (tp) REVERT: A 165 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6990 (mt) REVERT: A 396 GLN cc_start: 0.8563 (tp40) cc_final: 0.7649 (tt0) outliers start: 32 outliers final: 9 residues processed: 231 average time/residue: 0.0731 time to fit residues: 22.0695 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 459 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 ASN B 286 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS A 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.208164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.179614 restraints weight = 7555.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.176514 restraints weight = 11471.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.177065 restraints weight = 11051.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.176562 restraints weight = 9364.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.176722 restraints weight = 9407.455| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7056 Z= 0.159 Angle : 0.704 8.721 9646 Z= 0.337 Chirality : 0.040 0.157 1204 Planarity : 0.005 0.044 1118 Dihedral : 13.252 175.777 1529 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.46 % Allowed : 14.84 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.29), residues: 858 helix: 1.58 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.26 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 375 TYR 0.010 0.001 TYR A 223 PHE 0.015 0.001 PHE A 238 TRP 0.017 0.001 TRP A 171 HIS 0.002 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 ( 7056) covalent geometry : angle 0.70376 / 0.34 ( 9646) hydrogen bonds : bond 0.06895 / 4.50 ( 449) hydrogen bonds : angle 4.23644 / 3.09 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.231 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 200 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7056 (mmtt) REVERT: B 358 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.5719 (p90) REVERT: B 388 ILE cc_start: 0.8931 (mt) cc_final: 0.8694 (mm) REVERT: B 436 TYR cc_start: 0.7992 (t80) cc_final: 0.7586 (t80) REVERT: A 96 LEU cc_start: 0.8101 (tt) cc_final: 0.7836 (tp) REVERT: A 165 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7304 (mt) REVERT: A 358 PHE cc_start: 0.7019 (m-80) cc_final: 0.6798 (m-10) REVERT: A 396 GLN cc_start: 0.8597 (tp-100) cc_final: 0.7860 (tt0) REVERT: A 495 LEU cc_start: 0.7619 (mt) cc_final: 0.7415 (mt) outliers start: 24 outliers final: 15 residues processed: 168 average time/residue: 0.0801 time to fit residues: 17.9226 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 498 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.201646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.173169 restraints weight = 7640.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.170639 restraints weight = 11867.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170811 restraints weight = 11660.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.168973 restraints weight = 10051.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.169150 restraints weight = 10456.441| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7056 Z= 0.185 Angle : 0.705 7.577 9646 Z= 0.337 Chirality : 0.043 0.182 1204 Planarity : 0.005 0.040 1118 Dihedral : 12.549 174.668 1521 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.34 % Allowed : 13.98 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.29), residues: 858 helix: 1.61 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.26 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.012 0.002 TYR B 223 PHE 0.013 0.002 PHE B 115 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 7056) covalent geometry : angle 0.70502 / 0.34 ( 9646) hydrogen bonds : bond 0.06696 / 4.42 ( 449) hydrogen bonds : angle 4.19307 / 3.06 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.148 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 82 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4393 (tp) REVERT: B 358 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.5671 (p90) REVERT: B 436 TYR cc_start: 0.8044 (t80) cc_final: 0.7763 (t80) REVERT: A 82 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7078 (tp) REVERT: A 96 LEU cc_start: 0.8045 (tt) cc_final: 0.7830 (tp) REVERT: A 396 GLN cc_start: 0.8629 (tp-100) cc_final: 0.7893 (tt0) REVERT: A 510 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6651 (pt) outliers start: 44 outliers final: 26 residues processed: 160 average time/residue: 0.0731 time to fit residues: 15.7967 Evaluate side-chains 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.201129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.164797 restraints weight = 7589.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.161370 restraints weight = 11646.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.162903 restraints weight = 12535.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.162956 restraints weight = 9695.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.163289 restraints weight = 8802.517| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7056 Z= 0.144 Angle : 0.648 9.572 9646 Z= 0.308 Chirality : 0.040 0.163 1204 Planarity : 0.004 0.039 1118 Dihedral : 11.989 177.045 1519 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.76 % Allowed : 16.28 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.18 (0.30), residues: 858 helix: 1.72 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.19 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 475 TYR 0.015 0.002 TYR A 485 PHE 0.017 0.001 PHE A 153 TRP 0.009 0.001 TRP A 97 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7056) covalent geometry : angle 0.64758 / 0.31 ( 9646) hydrogen bonds : bond 0.05323 / 3.52 ( 449) hydrogen bonds : angle 3.95802 / 2.89 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.196 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 82 LEU cc_start: 0.4894 (OUTLIER) cc_final: 0.4560 (tp) REVERT: B 119 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6249 (mmp) REVERT: B 279 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7870 (mp) REVERT: B 358 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.5640 (p90) REVERT: B 456 TRP cc_start: 0.7968 (OUTLIER) cc_final: 0.6842 (m-90) REVERT: B 475 ARG cc_start: 0.7600 (ttm110) cc_final: 0.7339 (ptp-110) REVERT: B 477 HIS cc_start: 0.5673 (m-70) cc_final: 0.5053 (m-70) REVERT: A 396 GLN cc_start: 0.8605 (tp-100) cc_final: 0.7899 (tt0) REVERT: A 510 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6622 (pt) outliers start: 33 outliers final: 21 residues processed: 156 average time/residue: 0.0711 time to fit residues: 15.0730 Evaluate side-chains 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.203895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.166177 restraints weight = 7660.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.163693 restraints weight = 11072.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.166150 restraints weight = 10763.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.165603 restraints weight = 7575.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.166004 restraints weight = 8777.845| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7056 Z= 0.131 Angle : 0.616 6.856 9646 Z= 0.294 Chirality : 0.039 0.138 1204 Planarity : 0.004 0.039 1118 Dihedral : 11.486 178.522 1515 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.61 % Allowed : 16.57 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.33 (0.30), residues: 858 helix: 1.81 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.10 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.007 0.001 TYR A 260 PHE 0.011 0.001 PHE A 494 TRP 0.010 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7056) covalent geometry : angle 0.61597 / 0.29 ( 9646) hydrogen bonds : bond 0.04994 / 3.30 ( 449) hydrogen bonds : angle 3.86990 / 2.82 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.197 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 82 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4657 (tp) REVERT: B 279 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7785 (mp) REVERT: B 358 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5630 (p90) REVERT: B 456 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.6875 (m-90) REVERT: B 475 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7374 (ptp-110) REVERT: B 477 HIS cc_start: 0.5724 (m-70) cc_final: 0.5015 (m-70) REVERT: A 291 MET cc_start: 0.5263 (mmp) cc_final: 0.4932 (mtt) REVERT: A 396 GLN cc_start: 0.8548 (tp-100) cc_final: 0.7819 (tt0) REVERT: A 510 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6596 (pt) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 0.0730 time to fit residues: 15.0682 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.202020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.169645 restraints weight = 7708.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.166298 restraints weight = 10827.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.168196 restraints weight = 12292.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.168223 restraints weight = 8573.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.167972 restraints weight = 8994.833| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7056 Z= 0.177 Angle : 0.681 8.123 9646 Z= 0.328 Chirality : 0.042 0.174 1204 Planarity : 0.004 0.039 1118 Dihedral : 11.524 178.108 1515 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.76 % Allowed : 16.28 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.29), residues: 858 helix: 1.60 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.25 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.015 0.002 TYR A 485 PHE 0.015 0.001 PHE A 153 TRP 0.010 0.001 TRP A 97 HIS 0.005 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7056) covalent geometry : angle 0.68115 / 0.33 ( 9646) hydrogen bonds : bond 0.05838 / 3.86 ( 449) hydrogen bonds : angle 4.02874 / 2.94 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.175 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.4892 (OUTLIER) cc_final: 0.4564 (tp) REVERT: B 279 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7818 (mp) REVERT: B 358 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5699 (p90) REVERT: B 456 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.6964 (m-90) REVERT: B 477 HIS cc_start: 0.5640 (m-70) cc_final: 0.4878 (m-70) REVERT: A 155 ILE cc_start: 0.8172 (mm) cc_final: 0.7949 (mt) REVERT: A 396 GLN cc_start: 0.8562 (tp-100) cc_final: 0.7871 (tt0) REVERT: A 510 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6708 (pt) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.0709 time to fit residues: 14.9895 Evaluate side-chains 158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.200256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.167095 restraints weight = 7594.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.164533 restraints weight = 10656.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.167044 restraints weight = 11068.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.164624 restraints weight = 7964.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.165932 restraints weight = 8592.057| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7056 Z= 0.131 Angle : 0.615 6.482 9646 Z= 0.297 Chirality : 0.039 0.149 1204 Planarity : 0.004 0.037 1118 Dihedral : 11.299 179.549 1515 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.18 % Allowed : 17.15 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.29 (0.30), residues: 858 helix: 1.80 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.18 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.019 0.001 TYR A 485 PHE 0.010 0.001 PHE A 494 TRP 0.012 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7056) covalent geometry : angle 0.61494 / 0.30 ( 9646) hydrogen bonds : bond 0.04923 / 3.26 ( 449) hydrogen bonds : angle 3.89006 / 2.84 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.223 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5115 (OUTLIER) cc_final: 0.4798 (tp) REVERT: B 223 TYR cc_start: 0.7363 (t80) cc_final: 0.7153 (t80) REVERT: B 279 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7748 (mp) REVERT: B 358 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.5693 (p90) REVERT: B 456 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.6835 (m-90) REVERT: B 477 HIS cc_start: 0.5651 (m-70) cc_final: 0.4973 (m-70) REVERT: A 291 MET cc_start: 0.5188 (mmp) cc_final: 0.4786 (mtt) REVERT: A 396 GLN cc_start: 0.8542 (tp-100) cc_final: 0.7828 (tt0) REVERT: A 510 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6582 (pt) outliers start: 29 outliers final: 23 residues processed: 152 average time/residue: 0.0720 time to fit residues: 15.0822 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.202993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.167914 restraints weight = 7558.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.163749 restraints weight = 10449.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.164405 restraints weight = 12046.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.164180 restraints weight = 10753.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.164787 restraints weight = 9264.312| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7056 Z= 0.117 Angle : 0.595 7.517 9646 Z= 0.288 Chirality : 0.038 0.160 1204 Planarity : 0.004 0.036 1118 Dihedral : 10.999 179.915 1515 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.32 % Allowed : 17.72 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.56 (0.30), residues: 858 helix: 1.97 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.01 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 156 TYR 0.018 0.001 TYR A 485 PHE 0.011 0.001 PHE A 153 TRP 0.013 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 7056) covalent geometry : angle 0.59454 / 0.29 ( 9646) hydrogen bonds : bond 0.04196 / 2.77 ( 449) hydrogen bonds : angle 3.76432 / 2.75 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.264 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.4715 (tp) REVERT: B 358 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5601 (p90) REVERT: B 456 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.6889 (m-90) REVERT: B 477 HIS cc_start: 0.5475 (m-70) cc_final: 0.4855 (m-70) REVERT: A 291 MET cc_start: 0.5107 (mmp) cc_final: 0.4699 (mtt) REVERT: A 396 GLN cc_start: 0.8467 (tp-100) cc_final: 0.7801 (tt0) REVERT: A 510 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6572 (pt) outliers start: 30 outliers final: 22 residues processed: 153 average time/residue: 0.0675 time to fit residues: 14.2298 Evaluate side-chains 153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.203004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.177248 restraints weight = 7633.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.171250 restraints weight = 12138.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.169158 restraints weight = 11955.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170884 restraints weight = 11190.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.170148 restraints weight = 9099.476| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7056 Z= 0.119 Angle : 0.606 7.632 9646 Z= 0.293 Chirality : 0.039 0.166 1204 Planarity : 0.004 0.035 1118 Dihedral : 10.791 178.625 1513 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.89 % Allowed : 18.30 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.30), residues: 858 helix: 1.98 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.01 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 475 TYR 0.020 0.001 TYR A 485 PHE 0.019 0.001 PHE A 494 TRP 0.011 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 7056) covalent geometry : angle 0.60626 / 0.29 ( 9646) hydrogen bonds : bond 0.04229 / 2.81 ( 449) hydrogen bonds : angle 3.74959 / 2.73 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.241 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4663 (tp) REVERT: B 358 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5628 (p90) REVERT: B 449 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7074 (mtpm) REVERT: B 456 TRP cc_start: 0.7959 (OUTLIER) cc_final: 0.6968 (m-90) REVERT: A 291 MET cc_start: 0.5079 (mmp) cc_final: 0.4719 (mtt) REVERT: A 396 GLN cc_start: 0.8453 (tp-100) cc_final: 0.7791 (tt0) REVERT: A 510 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6594 (pt) outliers start: 27 outliers final: 19 residues processed: 155 average time/residue: 0.0743 time to fit residues: 15.8437 Evaluate side-chains 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN A 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.205910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.180280 restraints weight = 7502.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.174697 restraints weight = 11096.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.170345 restraints weight = 11946.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.171452 restraints weight = 13217.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.171401 restraints weight = 9815.191| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7056 Z= 0.121 Angle : 0.616 7.829 9646 Z= 0.297 Chirality : 0.039 0.269 1204 Planarity : 0.004 0.035 1118 Dihedral : 10.695 178.197 1513 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.75 % Allowed : 18.73 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.55 (0.30), residues: 858 helix: 1.96 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.01 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 475 TYR 0.017 0.001 TYR A 485 PHE 0.011 0.001 PHE A 494 TRP 0.010 0.001 TRP A 97 HIS 0.003 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7056) covalent geometry : angle 0.61558 / 0.30 ( 9646) hydrogen bonds : bond 0.04247 / 2.82 ( 449) hydrogen bonds : angle 3.74665 / 2.73 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.267 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4646 (tp) REVERT: B 358 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.5626 (p90) REVERT: B 449 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7049 (mtpm) REVERT: B 456 TRP cc_start: 0.7947 (OUTLIER) cc_final: 0.6915 (m-90) REVERT: A 291 MET cc_start: 0.5067 (mmp) cc_final: 0.4676 (mtt) REVERT: A 396 GLN cc_start: 0.8444 (tp-100) cc_final: 0.7783 (tt0) REVERT: A 510 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6665 (pt) outliers start: 26 outliers final: 20 residues processed: 152 average time/residue: 0.0730 time to fit residues: 15.2038 Evaluate side-chains 156 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.203901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.167306 restraints weight = 7664.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.163377 restraints weight = 10148.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.165135 restraints weight = 11571.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.166342 restraints weight = 9300.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.166234 restraints weight = 8529.291| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7056 Z= 0.122 Angle : 0.616 8.037 9646 Z= 0.297 Chirality : 0.040 0.241 1204 Planarity : 0.004 0.035 1118 Dihedral : 10.612 178.992 1513 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.03 % Allowed : 18.73 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.54 (0.30), residues: 858 helix: 1.95 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 475 TYR 0.019 0.001 TYR A 485 PHE 0.017 0.001 PHE A 494 TRP 0.010 0.001 TRP A 97 HIS 0.002 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7056) covalent geometry : angle 0.61587 / 0.30 ( 9646) hydrogen bonds : bond 0.04263 / 2.84 ( 449) hydrogen bonds : angle 3.73893 / 2.72 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1080.09 seconds wall clock time: 19 minutes 20.17 seconds (1160.17 seconds total)