Starting phenix.real_space_refine on Wed Mar 12 12:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1k_13163/03_2025/7p1k_13163_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1k_13163/03_2025/7p1k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p1k_13163/03_2025/7p1k_13163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1k_13163/03_2025/7p1k_13163.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1k_13163/03_2025/7p1k_13163_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1k_13163/03_2025/7p1k_13163_trim.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 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: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 5.10, per 1000 atoms: 0.74 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.78 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: 1.88 Time building geometry restraints manager: 2.23 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 - 11.26: 21 11.26 - 15.01: 15 15.01 - 18.76: 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 119.68 100.92 18.76 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 119.68 101.10 18.58 3.00e+00 1.11e-01 3.84e+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 - 35.56: 4460 35.56 - 71.11: 92 71.11 - 106.67: 13 106.67 - 142.22: 6 142.22 - 177.78: 7 Dihedral angle restraints: 4578 sinusoidal: 2166 harmonic: 2412 Sorted by residual: dihedral pdb=" C7 T7X A 806 " pdb=" O13 T7X A 806 " pdb=" P1 T7X A 806 " pdb=" O12 T7X A 806 " ideal model delta sinusoidal sigma weight residual 91.36 -90.86 -177.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C7 T7X B1203 " pdb=" O13 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O11 T7X B1203 " ideal model delta sinusoidal sigma weight residual 318.06 147.62 170.44 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C7 T7X B1203 " pdb=" O13 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O12 T7X B1203 " ideal model delta sinusoidal sigma weight residual 91.36 -100.83 -167.81 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4575 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 79 through 517 or resid 801 or resid 804)) selection = (chain 'B' and (resid 79 through 517 or resid 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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= 0.885 Angle : 1.119 18.761 9646 Z= 0.459 Chirality : 0.053 0.370 1204 Planarity : 0.024 0.342 1118 Dihedral : 16.196 177.778 3042 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (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 TRP 0.020 0.001 TRP A 171 HIS 0.002 0.001 HIS A 169 PHE 0.005 0.001 PHE A 300 TYR 0.005 0.001 TYR A 260 ARG 0.002 0.000 ARG B 186 *********************** 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 : 0.761 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: 0.7726 (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: 0.8448 (tt) cc_final: 0.8126 (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: 0.7648 (tt0) outliers start: 32 outliers final: 9 residues processed: 231 average time/residue: 0.2089 time to fit residues: 61.9843 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 : 0.748 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4178 r_free = 0.4178 target = 0.208780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.176748 restraints weight = 7515.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.173201 restraints weight = 11088.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.174322 restraints weight = 12144.207| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2809 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= 0.182 Angle : 0.717 8.928 9646 Z= 0.343 Chirality : 0.040 0.151 1204 Planarity : 0.005 0.045 1118 Dihedral : 16.744 175.006 1661 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.46 % Allowed : 15.27 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 858 helix: 1.61 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.23 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 171 HIS 0.002 0.001 HIS B 169 PHE 0.013 0.001 PHE A 238 TYR 0.011 0.001 TYR A 223 ARG 0.006 0.001 ARG A 375 *********************** 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 174 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.816 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: 0.7528 (mtmt) cc_final: 0.7064 (mmtt) REVERT: B 358 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5707 (p90) REVERT: B 388 ILE cc_start: 0.8918 (mt) cc_final: 0.8691 (mm) REVERT: B 436 TYR cc_start: 0.7917 (t80) cc_final: 0.7543 (t80) REVERT: A 96 LEU cc_start: 0.8056 (tt) cc_final: 0.7809 (tp) REVERT: A 165 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7310 (mt) REVERT: A 358 PHE cc_start: 0.6992 (m-80) cc_final: 0.6783 (m-10) REVERT: A 396 GLN cc_start: 0.8642 (tp-100) cc_final: 0.7950 (tt0) REVERT: A 495 LEU cc_start: 0.7692 (mt) cc_final: 0.7460 (mt) outliers start: 24 outliers final: 15 residues processed: 166 average time/residue: 0.2109 time to fit residues: 47.2199 Evaluate side-chains 148 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.203382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.171101 restraints weight = 7668.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.167527 restraints weight = 11643.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.169269 restraints weight = 12541.382| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7056 Z= 0.203 Angle : 0.656 7.596 9646 Z= 0.313 Chirality : 0.040 0.150 1204 Planarity : 0.004 0.040 1118 Dihedral : 15.140 178.131 1653 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.76 % Allowed : 13.83 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.30), residues: 858 helix: 1.83 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.21 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 232 HIS 0.002 0.001 HIS B 477 PHE 0.011 0.001 PHE A 153 TYR 0.012 0.002 TYR B 223 ARG 0.004 0.001 ARG A 156 *********************** 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 182 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.373 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: 0.4661 (OUTLIER) cc_final: 0.4308 (tp) REVERT: B 200 LYS cc_start: 0.7627 (mtmt) cc_final: 0.6963 (mmtt) REVERT: B 355 TYR cc_start: 0.7829 (t80) cc_final: 0.7384 (t80) REVERT: B 358 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5581 (p90) REVERT: B 436 TYR cc_start: 0.8019 (t80) cc_final: 0.7747 (t80) REVERT: A 82 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7042 (tp) REVERT: A 96 LEU cc_start: 0.8065 (tt) cc_final: 0.7839 (tp) REVERT: A 396 GLN cc_start: 0.8577 (tp-100) cc_final: 0.7880 (tt0) REVERT: A 510 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6618 (pt) outliers start: 40 outliers final: 22 residues processed: 170 average time/residue: 0.2598 time to fit residues: 59.3295 Evaluate side-chains 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 308 GLU 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 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 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.202452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.168004 restraints weight = 7587.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.164196 restraints weight = 10317.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.165285 restraints weight = 10418.009| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 7056 Z= 0.181 Angle : 0.638 8.146 9646 Z= 0.303 Chirality : 0.039 0.170 1204 Planarity : 0.004 0.040 1118 Dihedral : 14.036 178.750 1651 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.18 % Allowed : 16.28 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 858 helix: 1.85 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.15 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 PHE 0.010 0.001 PHE A 494 TYR 0.015 0.002 TYR A 485 ARG 0.003 0.000 ARG A 156 *********************** 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 169 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.749 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: 0.4823 (OUTLIER) cc_final: 0.4455 (tp) REVERT: B 119 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6216 (mmp) REVERT: B 200 LYS cc_start: 0.7613 (mtmt) cc_final: 0.6934 (mmtt) REVERT: B 279 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 358 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5595 (p90) REVERT: B 456 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.6805 (m-90) REVERT: B 475 ARG cc_start: 0.7592 (ttm110) cc_final: 0.7278 (ptp-110) REVERT: B 477 HIS cc_start: 0.5633 (m-70) cc_final: 0.4928 (m-70) REVERT: A 396 GLN cc_start: 0.8572 (tp-100) cc_final: 0.7861 (tt0) REVERT: A 510 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6646 (pt) outliers start: 29 outliers final: 20 residues processed: 158 average time/residue: 0.1864 time to fit residues: 39.3861 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 498 ILE Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.204150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.176313 restraints weight = 7567.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.174450 restraints weight = 11116.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.174700 restraints weight = 11009.689| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3751 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= 0.190 Angle : 0.621 6.945 9646 Z= 0.297 Chirality : 0.039 0.141 1204 Planarity : 0.004 0.038 1118 Dihedral : 13.099 177.020 1647 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.61 % Allowed : 16.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.30), residues: 858 helix: 1.87 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.17 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 PHE 0.013 0.001 PHE A 153 TYR 0.008 0.001 TYR A 260 ARG 0.002 0.000 ARG A 156 *********************** 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 164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.791 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: 0.4658 (OUTLIER) cc_final: 0.4299 (tp) REVERT: B 200 LYS cc_start: 0.7595 (mtmt) cc_final: 0.6980 (mmtm) REVERT: B 279 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 358 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5605 (p90) REVERT: B 456 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.6878 (m-90) REVERT: B 475 ARG cc_start: 0.7520 (ttm110) cc_final: 0.7240 (ptp-110) REVERT: B 477 HIS cc_start: 0.5301 (m-70) cc_final: 0.4631 (m-70) REVERT: A 291 MET cc_start: 0.4948 (mmp) cc_final: 0.4626 (mtt) REVERT: A 396 GLN cc_start: 0.8520 (tp-100) cc_final: 0.7816 (tt0) REVERT: A 510 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6687 (pt) outliers start: 32 outliers final: 22 residues processed: 153 average time/residue: 0.1844 time to fit residues: 37.6231 Evaluate side-chains 159 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 279 ILE 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 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 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.204457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.166813 restraints weight = 7623.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.163605 restraints weight = 11261.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.165794 restraints weight = 11480.515| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7056 Z= 0.171 Angle : 0.603 8.556 9646 Z= 0.289 Chirality : 0.038 0.150 1204 Planarity : 0.004 0.037 1118 Dihedral : 12.651 179.009 1647 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.76 % Allowed : 17.00 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 858 helix: 1.93 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.08 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 97 HIS 0.003 0.001 HIS B 477 PHE 0.010 0.001 PHE A 494 TYR 0.007 0.001 TYR A 223 ARG 0.004 0.000 ARG A 156 *********************** 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 169 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.737 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: 0.4889 (OUTLIER) cc_final: 0.4558 (tp) REVERT: B 223 TYR cc_start: 0.7377 (t80) cc_final: 0.7145 (t80) REVERT: B 279 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 358 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.5623 (p90) REVERT: B 456 TRP cc_start: 0.7929 (OUTLIER) cc_final: 0.6863 (m-90) REVERT: B 475 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7348 (ptp-110) REVERT: B 477 HIS cc_start: 0.5655 (m-70) cc_final: 0.4998 (m-70) REVERT: A 291 MET cc_start: 0.5220 (mmp) cc_final: 0.4875 (mtt) REVERT: A 396 GLN cc_start: 0.8511 (tp-100) cc_final: 0.7806 (tt0) outliers start: 33 outliers final: 22 residues processed: 159 average time/residue: 0.1970 time to fit residues: 41.4959 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 462 VAL 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 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 498 ILE 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 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.0010 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 61 optimal weight: 0.0020 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.209973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.180586 restraints weight = 7601.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.177856 restraints weight = 10791.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.178777 restraints weight = 11132.040| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7056 Z= 0.143 Angle : 0.573 6.327 9646 Z= 0.278 Chirality : 0.038 0.220 1204 Planarity : 0.004 0.034 1118 Dihedral : 12.140 179.940 1645 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.75 % Allowed : 17.72 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.30), residues: 858 helix: 2.14 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -1.98 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 97 HIS 0.003 0.001 HIS B 477 PHE 0.012 0.001 PHE A 153 TYR 0.007 0.001 TYR A 223 ARG 0.004 0.000 ARG B 156 *********************** 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 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.699 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: 0.4954 (OUTLIER) cc_final: 0.4471 (tp) REVERT: B 286 ASN cc_start: 0.7251 (m-40) cc_final: 0.7046 (m110) REVERT: B 358 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5428 (p90) REVERT: B 475 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7218 (ptp-110) REVERT: B 477 HIS cc_start: 0.5500 (m-70) cc_final: 0.4903 (m-70) REVERT: A 291 MET cc_start: 0.5068 (mmp) cc_final: 0.4681 (mtt) REVERT: A 396 GLN cc_start: 0.8445 (tp-100) cc_final: 0.7795 (tt0) outliers start: 26 outliers final: 12 residues processed: 148 average time/residue: 0.1763 time to fit residues: 35.2271 Evaluate side-chains 141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 358 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 262 VAL 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 516 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.207599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.178884 restraints weight = 7686.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.175986 restraints weight = 10413.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.175526 restraints weight = 11181.074| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7056 Z= 0.162 Angle : 0.596 6.922 9646 Z= 0.288 Chirality : 0.038 0.166 1204 Planarity : 0.004 0.034 1118 Dihedral : 11.987 179.847 1645 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.03 % Allowed : 18.88 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.30), residues: 858 helix: 2.07 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.00 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 PHE 0.019 0.001 PHE A 494 TYR 0.014 0.001 TYR B 223 ARG 0.004 0.000 ARG A 156 *********************** 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 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.653 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: 0.4674 (OUTLIER) cc_final: 0.4352 (tp) REVERT: B 200 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6934 (mmtm) REVERT: B 456 TRP cc_start: 0.7911 (OUTLIER) cc_final: 0.6954 (m-90) REVERT: B 475 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7120 (ptp-110) REVERT: B 477 HIS cc_start: 0.5474 (m-70) cc_final: 0.4920 (m-70) REVERT: A 291 MET cc_start: 0.5165 (mmp) cc_final: 0.4753 (mtt) REVERT: A 396 GLN cc_start: 0.8485 (tp-100) cc_final: 0.7811 (tt0) outliers start: 21 outliers final: 16 residues processed: 146 average time/residue: 0.1737 time to fit residues: 34.1686 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 406 GLU 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 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 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 516 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.205166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.178584 restraints weight = 7597.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.174233 restraints weight = 11688.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.171383 restraints weight = 10379.292| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7056 Z= 0.176 Angle : 0.607 6.930 9646 Z= 0.292 Chirality : 0.039 0.163 1204 Planarity : 0.004 0.033 1118 Dihedral : 11.869 179.830 1645 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.03 % Allowed : 18.73 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 858 helix: 2.00 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.04 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 232 HIS 0.004 0.001 HIS B 477 PHE 0.018 0.001 PHE A 494 TYR 0.007 0.001 TYR B 260 ARG 0.003 0.000 ARG A 156 *********************** 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 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.743 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: 0.4871 (OUTLIER) cc_final: 0.4538 (tp) REVERT: B 200 LYS cc_start: 0.7659 (mtmt) cc_final: 0.6947 (mmtm) REVERT: B 456 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6931 (m-90) REVERT: B 475 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7224 (ptp-110) REVERT: B 477 HIS cc_start: 0.5475 (m-70) cc_final: 0.4882 (m-70) REVERT: A 291 MET cc_start: 0.5261 (mmp) cc_final: 0.4879 (mtt) REVERT: A 396 GLN cc_start: 0.8477 (tp-100) cc_final: 0.7807 (tt0) outliers start: 21 outliers final: 18 residues processed: 149 average time/residue: 0.1844 time to fit residues: 37.0311 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain B residue 439 VAL 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 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 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 516 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 42 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.209895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.178999 restraints weight = 7551.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.176446 restraints weight = 11424.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.177555 restraints weight = 11366.644| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7056 Z= 0.199 Angle : 0.636 7.579 9646 Z= 0.307 Chirality : 0.040 0.159 1204 Planarity : 0.004 0.035 1118 Dihedral : 11.857 179.732 1645 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.46 % Allowed : 17.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.30), residues: 858 helix: 1.90 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.09 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 232 HIS 0.004 0.001 HIS B 477 PHE 0.017 0.001 PHE A 494 TYR 0.014 0.001 TYR B 223 ARG 0.005 0.000 ARG A 156 ********************** 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 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.708 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: 0.4729 (OUTLIER) cc_final: 0.4401 (tp) REVERT: B 358 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.5576 (p90) REVERT: B 456 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.6945 (m-90) REVERT: B 475 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7236 (ptp-110) REVERT: B 477 HIS cc_start: 0.5317 (m-70) cc_final: 0.4727 (m-70) REVERT: A 291 MET cc_start: 0.5151 (mmp) cc_final: 0.4738 (mtt) REVERT: A 396 GLN cc_start: 0.8475 (tp-100) cc_final: 0.7793 (tt0) outliers start: 24 outliers final: 20 residues processed: 148 average time/residue: 0.1825 time to fit residues: 36.2699 Evaluate side-chains 153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 358 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 439 VAL 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 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 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 516 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.0050 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.211843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.184274 restraints weight = 7690.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.181464 restraints weight = 10511.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.179036 restraints weight = 11633.911| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7056 Z= 0.157 Angle : 0.605 8.160 9646 Z= 0.292 Chirality : 0.039 0.170 1204 Planarity : 0.004 0.035 1118 Dihedral : 11.654 179.109 1645 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.59 % Allowed : 18.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.30), residues: 858 helix: 2.01 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 PHE 0.017 0.001 PHE A 494 TYR 0.007 0.001 TYR A 223 ARG 0.003 0.000 ARG B 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.97 seconds wall clock time: 41 minutes 35.30 seconds (2495.30 seconds total)