Starting phenix.real_space_refine on Thu Jul 2 07:10:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.map" model { file = "/net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7en0_31197/07_2026/7en0_31197.cif" } resolution = 2.97 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= 1.000 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 3 5.49 5 S 48 5.16 5 C 4878 2.51 5 N 1137 2.21 5 O 1173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s 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: 7239 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 8, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 8, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 2399 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PLC': 1, 'SPH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 357 " occ=0.50 residue: pdb=" N AARG B 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 357 " occ=0.50 residue: pdb=" N AARG C 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 357 " occ=0.50 Time building chain proxies: 2.23, per 1000 atoms: 0.31 Number of scatterers: 7239 At special positions: 0 Unit cell: (106.845, 105.797, 62.85, 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 48 16.00 P 3 15.00 O 1173 8.00 N 1137 7.00 C 4878 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: 0.63 Conformation dependent library (CDL) restraints added in 672.1 milliseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 221 removed outlier: 3.986A pdb=" N CYS A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 4.409A pdb=" N ASN A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.109A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 removed outlier: 4.227A pdb=" N ALA A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 328 removed outlier: 3.544A pdb=" N SER A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 3.559A pdb=" N LEU A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.710A pdb=" N HIS A 342 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 343 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 3.731A pdb=" N PHE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 3.890A pdb=" N HIS A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.553A pdb=" N SER A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 403 " --> pdb=" O TYR A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 403' Processing helix chain 'A' and resid 404 through 418 Processing helix chain 'A' and resid 423 through 443 removed outlier: 3.708A pdb=" N VAL A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.658A pdb=" N THR A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 removed outlier: 3.561A pdb=" N MET A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 201 through 221 removed outlier: 3.985A pdb=" N CYS B 205 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 4.409A pdb=" N ASN B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 4.109A pdb=" N ILE B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 277 through 289 removed outlier: 4.227A pdb=" N ALA B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 328 removed outlier: 3.545A pdb=" N SER B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 3.560A pdb=" N LEU B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.709A pdb=" N HIS B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.731A pdb=" N PHE B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 382 removed outlier: 3.890A pdb=" N HIS B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.553A pdb=" N SER B 401 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 403 " --> pdb=" O TYR B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 403' Processing helix chain 'B' and resid 404 through 418 Processing helix chain 'B' and resid 423 through 443 removed outlier: 3.708A pdb=" N VAL B 441 " --> pdb=" O MET B 437 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.658A pdb=" N THR B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 507 removed outlier: 3.561A pdb=" N MET B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 201 through 221 removed outlier: 3.986A pdb=" N CYS C 205 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 259 removed outlier: 4.409A pdb=" N ASN C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 removed outlier: 4.110A pdb=" N ILE C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 264 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 276 Processing helix chain 'C' and resid 277 through 289 removed outlier: 4.226A pdb=" N ALA C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 289 " --> pdb=" O PHE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 328 removed outlier: 3.545A pdb=" N SER C 310 " --> pdb=" O VAL C 306 " (cutoff:3.500A) Proline residue: C 313 - end of helix removed outlier: 3.559A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 326 " --> pdb=" O TYR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.710A pdb=" N HIS C 342 " --> pdb=" O PRO C 339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 343 " --> pdb=" O SER C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 359 removed outlier: 3.731A pdb=" N PHE C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 382 removed outlier: 3.889A pdb=" N HIS C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 removed outlier: 3.553A pdb=" N SER C 401 " --> pdb=" O PRO C 398 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C 402 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 403 " --> pdb=" O TYR C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 398 through 403' Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'C' and resid 423 through 443 removed outlier: 3.708A pdb=" N VAL C 441 " --> pdb=" O MET C 437 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.658A pdb=" N THR C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 507 removed outlier: 3.561A pdb=" N MET C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1362 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: 1.17 Time building geometry restraints manager: 0.86 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: 1008 1.31 - 1.43: 2194 1.43 - 1.56: 4166 1.56 - 1.68: 6 1.68 - 1.81: 78 Bond restraints: 7452 Sorted by residual: bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PLC C 601 " pdb=" O3 PLC C 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C' PLC C 601 " pdb=" O2 PLC C 601 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 7447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 9939 3.17 - 6.33: 207 6.33 - 9.50: 21 9.50 - 12.66: 3 12.66 - 15.83: 3 Bond angle restraints: 10173 Sorted by residual: angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 109.45 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 109.44 -15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P PLC C 601 " pdb=" P PLC C 601 " pdb=" O4P PLC C 601 " ideal model delta sigma weight residual 93.62 109.43 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N LEU B 504 " pdb=" CA LEU B 504 " pdb=" C LEU B 504 " ideal model delta sigma weight residual 113.20 106.98 6.22 1.21e+00 6.83e-01 2.64e+01 angle pdb=" N LEU C 504 " pdb=" CA LEU C 504 " pdb=" C LEU C 504 " ideal model delta sigma weight residual 113.20 107.01 6.19 1.21e+00 6.83e-01 2.62e+01 ... (remaining 10168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 4041 28.40 - 56.80: 192 56.80 - 85.21: 3 85.21 - 113.61: 3 113.61 - 142.01: 3 Dihedral angle restraints: 4242 sinusoidal: 1491 harmonic: 2751 Sorted by residual: dihedral pdb=" C5 SPH B 602 " pdb=" C3 SPH B 602 " pdb=" C4 SPH B 602 " pdb=" O3 SPH B 602 " ideal model delta sinusoidal sigma weight residual -68.94 38.58 -107.52 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5 SPH A 602 " pdb=" C3 SPH A 602 " pdb=" C4 SPH A 602 " pdb=" O3 SPH A 602 " ideal model delta sinusoidal sigma weight residual -68.94 38.55 -107.49 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5 SPH C 602 " pdb=" C3 SPH C 602 " pdb=" C4 SPH C 602 " pdb=" O3 SPH C 602 " ideal model delta sinusoidal sigma weight residual -68.94 38.48 -107.42 1 2.00e+01 2.50e-03 3.12e+01 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 839 0.046 - 0.093: 268 0.093 - 0.139: 45 0.139 - 0.185: 15 0.185 - 0.231: 18 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA HIS A 506 " pdb=" N HIS A 506 " pdb=" C HIS A 506 " pdb=" CB HIS A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA HIS C 506 " pdb=" N HIS C 506 " pdb=" C HIS C 506 " pdb=" CB HIS C 506 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA HIS B 506 " pdb=" N HIS B 506 " pdb=" C HIS B 506 " pdb=" CB HIS B 506 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1182 not shown) Planarity restraints: 1215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 423 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ALA B 423 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 423 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 424 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 423 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ALA A 423 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 423 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 424 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 423 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C ALA C 423 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA C 423 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 424 " 0.013 2.00e-02 2.50e+03 ... (remaining 1212 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2269 2.82 - 3.34: 6826 3.34 - 3.86: 12171 3.86 - 4.38: 14508 4.38 - 4.90: 24431 Nonbonded interactions: 60205 Sorted by model distance: nonbonded pdb=" O THR B 459 " pdb=" OG1 THR B 463 " model vdw 2.299 3.040 nonbonded pdb=" O THR A 459 " pdb=" OG1 THR A 463 " model vdw 2.300 3.040 nonbonded pdb=" O THR C 459 " pdb=" OG1 THR C 463 " model vdw 2.300 3.040 nonbonded pdb=" O SER C 340 " pdb=" OG SER C 340 " model vdw 2.324 3.040 nonbonded pdb=" O SER B 340 " pdb=" OG SER B 340 " model vdw 2.325 3.040 ... (remaining 60200 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.38 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.070 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.006 0.071 7452 Z= 0.362 Angle : 1.058 15.827 10173 Z= 0.596 Chirality : 0.053 0.231 1185 Planarity : 0.005 0.031 1215 Dihedral : 15.940 142.011 2460 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.21 % Favored : 95.15 % Rotamer: Outliers : 4.80 % Allowed : 15.72 % Favored : 79.48 % 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: -3.26 (0.25), residues: 936 helix: -2.04 (0.17), residues: 681 sheet: None (None), residues: 0 loop : -1.92 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 225 TYR 0.007 0.001 TYR C 400 PHE 0.017 0.001 PHE A 421 TRP 0.008 0.001 TRP B 215 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.36 ( 7452) covalent geometry : angle 1.05762 / 0.60 (10173) hydrogen bonds : bond 0.17744 / 11.69 ( 483) hydrogen bonds : angle 6.69506 / 4.71 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7285 (mt) REVERT: A 332 ARG cc_start: 0.6296 (ttp-110) cc_final: 0.5481 (ttt90) REVERT: A 482 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6940 (mtm-85) REVERT: A 491 MET cc_start: 0.7328 (ttm) cc_final: 0.7032 (ttm) REVERT: A 505 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6175 (mp) REVERT: B 263 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7086 (mt) REVERT: B 264 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6534 (mtm180) REVERT: B 327 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (p) REVERT: B 332 ARG cc_start: 0.6177 (ttp-110) cc_final: 0.5386 (ttt90) REVERT: B 491 MET cc_start: 0.7502 (ttm) cc_final: 0.7290 (ttm) REVERT: B 505 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5963 (mp) REVERT: C 264 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6416 (ttp-110) REVERT: C 267 PHE cc_start: 0.7844 (t80) cc_final: 0.7498 (t80) REVERT: C 272 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6666 (mtt180) REVERT: C 331 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.5703 (mmm160) REVERT: C 332 ARG cc_start: 0.6126 (ttp-110) cc_final: 0.5264 (ttt90) REVERT: C 455 TRP cc_start: 0.6427 (t-100) cc_final: 0.6210 (t-100) REVERT: C 482 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7153 (ttm-80) REVERT: C 505 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6048 (mp) outliers start: 30 outliers final: 7 residues processed: 148 average time/residue: 0.5397 time to fit residues: 84.3890 Evaluate side-chains 118 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 HIS A 348 ASN A 374 HIS B 348 ASN B 374 HIS C 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.155977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111457 restraints weight = 25306.542| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.97 r_work: 0.2835 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7452 Z= 0.130 Angle : 0.605 9.806 10173 Z= 0.295 Chirality : 0.038 0.119 1185 Planarity : 0.005 0.029 1215 Dihedral : 13.988 137.956 1141 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.33 % Allowed : 21.83 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.17 (0.27), residues: 936 helix: -0.46 (0.19), residues: 681 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 331 TYR 0.019 0.002 TYR B 259 PHE 0.019 0.001 PHE B 260 TRP 0.017 0.001 TRP B 455 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7452) covalent geometry : angle 0.60499 / 0.29 (10173) hydrogen bonds : bond 0.03909 / 2.65 ( 483) hydrogen bonds : angle 4.16082 / 2.98 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 264 ARG cc_start: 0.6453 (mtm-85) cc_final: 0.6154 (ttp-110) REVERT: A 332 ARG cc_start: 0.6221 (ttp-110) cc_final: 0.5336 (ttt90) REVERT: C 264 ARG cc_start: 0.6504 (mtm-85) cc_final: 0.6268 (mtm180) REVERT: C 272 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7377 (mtt180) REVERT: C 501 VAL cc_start: 0.7889 (m) cc_final: 0.7638 (t) REVERT: C 505 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6143 (mp) outliers start: 13 outliers final: 3 residues processed: 108 average time/residue: 0.6416 time to fit residues: 72.6733 Evaluate side-chains 95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 80 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.154342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109091 restraints weight = 22602.549| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.64 r_work: 0.2864 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7452 Z= 0.119 Angle : 0.572 10.223 10173 Z= 0.276 Chirality : 0.037 0.121 1185 Planarity : 0.004 0.029 1215 Dihedral : 12.885 131.180 1121 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.75 % Allowed : 24.60 % Favored : 73.65 % 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: -0.06 (0.28), residues: 936 helix: 0.26 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 331 TYR 0.016 0.001 TYR C 259 PHE 0.027 0.001 PHE C 267 TRP 0.021 0.001 TRP B 455 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7452) covalent geometry : angle 0.57188 / 0.28 (10173) hydrogen bonds : bond 0.03729 / 2.51 ( 483) hydrogen bonds : angle 3.90063 / 2.79 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 264 ARG cc_start: 0.6417 (mtm-85) cc_final: 0.6054 (ttp-110) REVERT: A 331 ARG cc_start: 0.7487 (mpp80) cc_final: 0.6108 (mmm160) REVERT: A 332 ARG cc_start: 0.6092 (ttp-110) cc_final: 0.5238 (ttt90) REVERT: A 505 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6226 (mp) REVERT: B 224 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.6492 (mmm) REVERT: B 314 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 414 TRP cc_start: 0.9240 (t-100) cc_final: 0.9035 (t-100) REVERT: C 272 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7391 (mtt180) REVERT: C 501 VAL cc_start: 0.7825 (m) cc_final: 0.7609 (t) REVERT: C 505 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.6001 (mp) outliers start: 9 outliers final: 1 residues processed: 102 average time/residue: 0.6135 time to fit residues: 65.7263 Evaluate side-chains 98 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.154445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109510 restraints weight = 28126.163| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.54 r_work: 0.2747 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7452 Z= 0.119 Angle : 0.562 9.449 10173 Z= 0.270 Chirality : 0.037 0.123 1185 Planarity : 0.004 0.029 1215 Dihedral : 12.282 125.663 1121 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.75 % Allowed : 25.33 % Favored : 72.93 % 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: 0.46 (0.29), residues: 936 helix: 0.65 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.38 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.020 0.001 TYR A 259 PHE 0.022 0.001 PHE C 267 TRP 0.026 0.001 TRP B 455 HIS 0.002 0.001 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7452) covalent geometry : angle 0.56175 / 0.27 (10173) hydrogen bonds : bond 0.03646 / 2.46 ( 483) hydrogen bonds : angle 3.79237 / 2.71 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.253 Fit side-chains REVERT: A 264 ARG cc_start: 0.6336 (mtm-85) cc_final: 0.5985 (ttp-110) REVERT: A 331 ARG cc_start: 0.7437 (mpp80) cc_final: 0.6095 (mmm160) REVERT: A 332 ARG cc_start: 0.6116 (ttp-110) cc_final: 0.5233 (ttt90) REVERT: A 505 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6274 (mp) REVERT: C 264 ARG cc_start: 0.6468 (ttp-110) cc_final: 0.6160 (ttp-110) REVERT: C 272 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7396 (mtt180) REVERT: C 505 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5910 (mp) outliers start: 9 outliers final: 0 residues processed: 101 average time/residue: 0.6228 time to fit residues: 66.1339 Evaluate side-chains 93 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.153751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109323 restraints weight = 22876.461| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.58 r_work: 0.2844 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7452 Z= 0.126 Angle : 0.558 8.612 10173 Z= 0.269 Chirality : 0.038 0.124 1185 Planarity : 0.004 0.029 1215 Dihedral : 11.948 120.483 1121 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.89 % Allowed : 26.20 % Favored : 71.91 % 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: 0.78 (0.29), residues: 936 helix: 0.88 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.26 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.021 0.001 TYR B 259 PHE 0.023 0.001 PHE B 479 TRP 0.025 0.001 TRP B 455 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7452) covalent geometry : angle 0.55795 / 0.27 (10173) hydrogen bonds : bond 0.03703 / 2.49 ( 483) hydrogen bonds : angle 3.77381 / 2.70 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.310 Fit side-chains REVERT: A 331 ARG cc_start: 0.7446 (mpp80) cc_final: 0.6190 (mmm160) REVERT: A 332 ARG cc_start: 0.6260 (ttp-110) cc_final: 0.5414 (ttt90) REVERT: A 421 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: A 505 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6217 (mp) REVERT: B 331 ARG cc_start: 0.7369 (mpp80) cc_final: 0.6101 (mmm160) REVERT: C 264 ARG cc_start: 0.6454 (ttp-110) cc_final: 0.6128 (ttp-110) REVERT: C 272 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7282 (mtt180) outliers start: 10 outliers final: 1 residues processed: 103 average time/residue: 0.5983 time to fit residues: 64.9911 Evaluate side-chains 96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 421 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN C 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104732 restraints weight = 22819.360| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.49 r_work: 0.2782 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7452 Z= 0.173 Angle : 0.601 8.151 10173 Z= 0.291 Chirality : 0.040 0.129 1185 Planarity : 0.004 0.029 1215 Dihedral : 11.979 117.615 1119 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.75 % Allowed : 26.64 % Favored : 71.62 % 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: 0.85 (0.29), residues: 936 helix: 0.91 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.15 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 264 TYR 0.015 0.001 TYR A 259 PHE 0.022 0.001 PHE C 479 TRP 0.027 0.001 TRP B 455 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 7452) covalent geometry : angle 0.60069 / 0.29 (10173) hydrogen bonds : bond 0.04091 / 2.76 ( 483) hydrogen bonds : angle 3.90032 / 2.78 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.237 Fit side-chains REVERT: A 331 ARG cc_start: 0.7480 (mpp80) cc_final: 0.6140 (mmm160) REVERT: A 332 ARG cc_start: 0.6570 (ttp-110) cc_final: 0.5646 (ttt90) REVERT: A 505 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6193 (mp) REVERT: B 224 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.6607 (mtm) REVERT: B 331 ARG cc_start: 0.7405 (mpp80) cc_final: 0.6165 (mmm160) REVERT: B 332 ARG cc_start: 0.6352 (ttp-110) cc_final: 0.5461 (ttt90) REVERT: C 224 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.6405 (mmm) REVERT: C 264 ARG cc_start: 0.6581 (ttp-110) cc_final: 0.6171 (ttp-110) REVERT: C 272 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7261 (mtt180) outliers start: 9 outliers final: 2 residues processed: 99 average time/residue: 0.6249 time to fit residues: 64.9947 Evaluate side-chains 96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 421 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.152797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108435 restraints weight = 31163.215| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 5.90 r_work: 0.2673 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7452 Z= 0.123 Angle : 0.558 7.639 10173 Z= 0.271 Chirality : 0.038 0.122 1185 Planarity : 0.003 0.029 1215 Dihedral : 11.154 107.941 1119 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.75 % Allowed : 27.51 % Favored : 70.74 % 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: 1.13 (0.29), residues: 936 helix: 1.12 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.08 (0.46), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 264 TYR 0.016 0.001 TYR A 259 PHE 0.020 0.001 PHE C 479 TRP 0.026 0.001 TRP B 455 HIS 0.002 0.001 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7452) covalent geometry : angle 0.55754 / 0.27 (10173) hydrogen bonds : bond 0.03644 / 2.46 ( 483) hydrogen bonds : angle 3.79140 / 2.71 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.233 Fit side-chains REVERT: A 331 ARG cc_start: 0.7369 (mpp80) cc_final: 0.5963 (mmm160) REVERT: A 332 ARG cc_start: 0.6334 (ttp-110) cc_final: 0.5415 (ttt90) REVERT: A 421 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: A 505 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5974 (mp) REVERT: B 224 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.6502 (mtm) REVERT: B 331 ARG cc_start: 0.7333 (mpp80) cc_final: 0.5939 (mmm160) REVERT: B 332 ARG cc_start: 0.6047 (ttp-110) cc_final: 0.5183 (ttt90) REVERT: C 264 ARG cc_start: 0.6433 (ttp-110) cc_final: 0.5992 (ttp-110) REVERT: C 272 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7149 (mtt180) REVERT: C 421 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: C 462 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8342 (ptm) outliers start: 9 outliers final: 2 residues processed: 96 average time/residue: 0.5398 time to fit residues: 54.6299 Evaluate side-chains 101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 495 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106764 restraints weight = 27840.059| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 5.05 r_work: 0.2805 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7452 Z= 0.133 Angle : 0.565 6.937 10173 Z= 0.275 Chirality : 0.038 0.126 1185 Planarity : 0.004 0.030 1215 Dihedral : 10.752 95.282 1119 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.89 % Allowed : 27.37 % Favored : 70.74 % 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: 1.22 (0.29), residues: 936 helix: 1.17 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.01 (0.46), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.015 0.001 TYR A 259 PHE 0.019 0.001 PHE C 479 TRP 0.026 0.001 TRP B 455 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7452) covalent geometry : angle 0.56455 / 0.28 (10173) hydrogen bonds : bond 0.03748 / 2.53 ( 483) hydrogen bonds : angle 3.80518 / 2.71 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.156 Fit side-chains REVERT: A 331 ARG cc_start: 0.7429 (mpp80) cc_final: 0.6103 (mmm160) REVERT: A 332 ARG cc_start: 0.6388 (ttp-110) cc_final: 0.5484 (ttt90) REVERT: A 421 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 505 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5966 (mp) REVERT: B 224 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6574 (mtm) REVERT: B 331 ARG cc_start: 0.7416 (mpp80) cc_final: 0.6048 (mmm160) REVERT: B 332 ARG cc_start: 0.6150 (ttp-110) cc_final: 0.5291 (ttt90) REVERT: B 437 MET cc_start: 0.8340 (mtm) cc_final: 0.8038 (ptp) REVERT: C 264 ARG cc_start: 0.6524 (ttp-110) cc_final: 0.6069 (ttp-110) REVERT: C 272 ARG cc_start: 0.7393 (mtt180) cc_final: 0.7055 (mtt180) REVERT: C 421 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: C 462 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (ptm) outliers start: 10 outliers final: 3 residues processed: 98 average time/residue: 0.5631 time to fit residues: 58.1740 Evaluate side-chains 99 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 495 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 15 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108480 restraints weight = 27424.674| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 5.12 r_work: 0.2805 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (17 function evaluations) r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7452 Z= 0.118 Angle : 0.545 6.274 10173 Z= 0.269 Chirality : 0.038 0.123 1185 Planarity : 0.003 0.029 1215 Dihedral : 10.167 88.463 1119 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.75 % Allowed : 27.22 % Favored : 71.03 % 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: 1.41 (0.29), residues: 936 helix: 1.29 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.16 (0.47), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.015 0.001 TYR A 259 PHE 0.010 0.001 PHE C 226 TRP 0.024 0.001 TRP B 455 HIS 0.002 0.001 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7452) covalent geometry : angle 0.54507 / 0.27 (10173) hydrogen bonds : bond 0.03546 / 2.40 ( 483) hydrogen bonds : angle 3.73558 / 2.67 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.234 Fit side-chains REVERT: A 331 ARG cc_start: 0.7433 (mpp80) cc_final: 0.6096 (mmm160) REVERT: A 332 ARG cc_start: 0.6293 (ttp-110) cc_final: 0.5408 (ttt90) REVERT: A 421 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: A 431 MET cc_start: 0.8047 (ttm) cc_final: 0.7470 (mtp) REVERT: A 505 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5945 (mp) REVERT: B 331 ARG cc_start: 0.7380 (mpp80) cc_final: 0.6063 (mmm160) REVERT: B 437 MET cc_start: 0.8296 (mtm) cc_final: 0.8048 (ptp) REVERT: B 489 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8102 (m) REVERT: C 264 ARG cc_start: 0.6517 (ttp-110) cc_final: 0.6046 (ttp-110) REVERT: C 272 ARG cc_start: 0.7419 (mtt180) cc_final: 0.7089 (mtt180) REVERT: C 421 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: C 462 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8306 (ptm) outliers start: 9 outliers final: 3 residues processed: 104 average time/residue: 0.4479 time to fit residues: 49.2908 Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104361 restraints weight = 19399.331| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.77 r_work: 0.2701 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7452 Z= 0.195 Angle : 0.617 7.009 10173 Z= 0.304 Chirality : 0.041 0.131 1185 Planarity : 0.004 0.031 1215 Dihedral : 10.334 89.969 1119 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.89 % Allowed : 27.37 % Favored : 70.74 % 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: 1.08 (0.29), residues: 936 helix: 1.03 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.09 (0.47), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.015 0.001 TYR A 259 PHE 0.026 0.002 PHE B 479 TRP 0.027 0.002 TRP B 455 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 7452) covalent geometry : angle 0.61684 / 0.30 (10173) hydrogen bonds : bond 0.04257 / 2.87 ( 483) hydrogen bonds : angle 3.95696 / 2.82 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.263 Fit side-chains REVERT: A 331 ARG cc_start: 0.7557 (mpp80) cc_final: 0.6169 (mmm160) REVERT: A 332 ARG cc_start: 0.6504 (ttp-110) cc_final: 0.5596 (ttt90) REVERT: A 490 LEU cc_start: 0.7991 (tp) cc_final: 0.7596 (mm) REVERT: A 505 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6143 (mp) REVERT: B 331 ARG cc_start: 0.7447 (mpp80) cc_final: 0.6097 (mmm160) REVERT: B 332 ARG cc_start: 0.6315 (ttp-110) cc_final: 0.5434 (ttt90) REVERT: C 264 ARG cc_start: 0.6570 (ttp-110) cc_final: 0.6095 (ttp-110) REVERT: C 272 ARG cc_start: 0.7455 (mtt180) cc_final: 0.7122 (mtt180) REVERT: C 462 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8296 (ptm) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.5255 time to fit residues: 56.3242 Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.151954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107538 restraints weight = 23969.561| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.41 r_work: 0.2757 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7452 Z= 0.132 Angle : 0.570 6.189 10173 Z= 0.281 Chirality : 0.038 0.124 1185 Planarity : 0.003 0.030 1215 Dihedral : 9.837 83.276 1119 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.60 % Allowed : 27.80 % Favored : 70.60 % 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 (0.29), residues: 936 helix: 1.18 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.18 (0.47), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.016 0.001 TYR A 259 PHE 0.024 0.001 PHE C 479 TRP 0.026 0.001 TRP B 455 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7452) covalent geometry : angle 0.56956 / 0.28 (10173) hydrogen bonds : bond 0.03776 / 2.55 ( 483) hydrogen bonds : angle 3.85047 / 2.74 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.94 seconds wall clock time: 42 minutes 26.70 seconds (2546.70 seconds total)