Starting phenix.real_space_refine on Mon Mar 11 05:22:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzx_36754/03_2024/8jzx_36754_updated.pdb" } resolution = 2.5 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= -0.001 sd= 0.058 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4760 2.51 5 N 1126 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3452 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3452 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'CLR': 2, 'NAG': 1, 'Q09': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'CLR': 2, 'NAG': 1, 'Q09': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.18, per 1000 atoms: 0.59 Number of scatterers: 7108 At special positions: 0 Unit cell: (80.9568, 59.031, 124.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1186 8.00 N 1126 7.00 C 4760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 436 " " NAG B 601 " - " ASN B 436 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 2 sheets defined 73.8% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 34 through 55 removed outlier: 3.810A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 71 through 87 removed outlier: 3.568A pdb=" N TYR A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.836A pdb=" N ALA A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 117 through 124 Proline residue: A 121 - end of helix removed outlier: 3.572A pdb=" N ALA A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 4.513A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 180 removed outlier: 3.611A pdb=" N ALA A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.790A pdb=" N ALA A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 3.964A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.631A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Proline residue: A 229 - end of helix removed outlier: 3.857A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 3.561A pdb=" N VAL A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 329 through 347 removed outlier: 3.578A pdb=" N GLN A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.501A pdb=" N LEU A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.912A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 391 through 394 No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 401 through 429 removed outlier: 3.527A pdb=" N MET A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 478 removed outlier: 3.650A pdb=" N VAL A 455 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Proline residue: A 456 - end of helix removed outlier: 3.963A pdb=" N LEU A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 461 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 463 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 464 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER A 469 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 470 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 475 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 532 through 557 removed outlier: 3.627A pdb=" N ILE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 34 through 55 removed outlier: 3.810A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 71 through 87 removed outlier: 3.568A pdb=" N TYR B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.836A pdb=" N ALA B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.573A pdb=" N ALA B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 4.513A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 180 removed outlier: 3.612A pdb=" N ALA B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 3.790A pdb=" N ALA B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 211 removed outlier: 3.965A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 removed outlier: 3.631A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Proline residue: B 229 - end of helix removed outlier: 3.857A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 3.562A pdb=" N VAL B 319 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 329 through 347 removed outlier: 3.577A pdb=" N GLN B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.500A pdb=" N LEU B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 removed outlier: 3.912A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.527A pdb=" N MET B 413 " --> pdb=" O MET B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 478 removed outlier: 3.650A pdb=" N VAL B 455 " --> pdb=" O TRP B 452 " (cutoff:3.500A) Proline residue: B 456 - end of helix removed outlier: 3.963A pdb=" N LEU B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE B 461 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 463 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 464 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER B 469 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 476 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 478 " --> pdb=" O PHE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 Processing helix chain 'B' and resid 532 through 557 removed outlier: 3.626A pdb=" N ILE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 435 through 439 removed outlier: 3.834A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 435 through 439 removed outlier: 3.834A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1134 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: 1.83 Time building geometry restraints manager: 3.12 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: 1048 1.31 - 1.43: 2025 1.43 - 1.56: 4165 1.56 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 7292 Sorted by residual: bond pdb=" C25 Q09 B 604 " pdb=" N26 Q09 B 604 " ideal model delta sigma weight residual 1.453 1.212 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C25 Q09 A 603 " pdb=" N26 Q09 A 603 " ideal model delta sigma weight residual 1.453 1.212 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C ILE A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C ILE B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 1.335 1.381 -0.047 1.19e-02 7.06e+03 1.54e+01 bond pdb=" C27 Q09 B 604 " pdb=" N26 Q09 B 604 " ideal model delta sigma weight residual 1.489 1.441 0.048 2.00e-02 2.50e+03 5.82e+00 ... (remaining 7287 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.82: 140 104.82 - 112.12: 3599 112.12 - 119.43: 2381 119.43 - 126.74: 3715 126.74 - 134.04: 105 Bond angle restraints: 9940 Sorted by residual: angle pdb=" C ALA B 29 " pdb=" N PHE B 30 " pdb=" CA PHE B 30 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" C ALA A 29 " pdb=" N PHE A 30 " pdb=" CA PHE A 30 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" C PHE A 30 " pdb=" N ALA A 31 " pdb=" CA ALA A 31 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C PHE B 30 " pdb=" N ALA B 31 " pdb=" CA ALA B 31 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C GLN B 485 " pdb=" N SER B 486 " pdb=" CA SER B 486 " ideal model delta sigma weight residual 121.54 130.07 -8.53 1.91e+00 2.74e-01 1.99e+01 ... (remaining 9935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4206 17.87 - 35.73: 166 35.73 - 53.60: 22 53.60 - 71.47: 8 71.47 - 89.33: 4 Dihedral angle restraints: 4406 sinusoidal: 1810 harmonic: 2596 Sorted by residual: dihedral pdb=" CA PHE B 30 " pdb=" C PHE B 30 " pdb=" N ALA B 31 " pdb=" CA ALA B 31 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PHE A 30 " pdb=" C PHE A 30 " pdb=" N ALA A 31 " pdb=" CA ALA A 31 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO B 390 " pdb=" C PRO B 390 " pdb=" N ILE B 391 " pdb=" CA ILE B 391 " ideal model delta harmonic sigma weight residual 180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1056 0.082 - 0.164: 92 0.164 - 0.245: 18 0.245 - 0.327: 6 0.327 - 0.409: 4 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C13 CLR A 604 " pdb=" C12 CLR A 604 " pdb=" C14 CLR A 604 " pdb=" C17 CLR A 604 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C13 CLR B 602 " pdb=" C12 CLR B 602 " pdb=" C14 CLR B 602 " pdb=" C17 CLR B 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.53 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C14 CLR B 602 " pdb=" C13 CLR B 602 " pdb=" C15 CLR B 602 " pdb=" C8 CLR B 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1173 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 536 " -0.018 2.00e-02 2.50e+03 1.79e-02 5.58e+00 pdb=" CG PHE B 536 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 536 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 536 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 536 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 536 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 536 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 536 " 0.017 2.00e-02 2.50e+03 1.77e-02 5.49e+00 pdb=" CG PHE A 536 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 536 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 536 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 536 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 536 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 536 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 120 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 121 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.029 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2223 2.82 - 3.34: 6566 3.34 - 3.86: 11745 3.86 - 4.38: 14496 4.38 - 4.90: 24455 Nonbonded interactions: 59485 Sorted by model distance: nonbonded pdb=" C21 CLR A 602 " pdb=" C23 CLR A 602 " model vdw 2.300 3.088 nonbonded pdb=" C21 CLR B 603 " pdb=" C23 CLR B 603 " model vdw 2.301 3.088 nonbonded pdb=" O ALA A 27 " pdb=" NH1 ARG A 193 " model vdw 2.367 2.520 nonbonded pdb=" O ALA B 27 " pdb=" NH1 ARG B 193 " model vdw 2.368 2.520 nonbonded pdb=" O PHE B 30 " pdb=" N GLY B 32 " model vdw 2.385 2.520 ... (remaining 59480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 558 or resid 601 through 602)) selection = (chain 'B' and (resid 18 through 558 or resid 601 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 7.060 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.410 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.008 0.241 7292 Z= 0.514 Angle : 1.147 11.637 9940 Z= 0.583 Chirality : 0.060 0.409 1176 Planarity : 0.007 0.050 1188 Dihedral : 10.907 89.333 2736 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.07 % Favored : 93.71 % Rotamer: Outliers : 0.28 % Allowed : 1.14 % Favored : 98.58 % 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: -6.11 (0.16), residues: 890 helix: -4.21 (0.09), residues: 652 sheet: None (None), residues: 0 loop : -2.69 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 368 HIS 0.002 0.001 HIS A 362 PHE 0.040 0.003 PHE B 536 TYR 0.027 0.003 TYR B 113 ARG 0.008 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.7655 (m-10) cc_final: 0.7366 (t80) REVERT: B 73 GLN cc_start: 0.7785 (mt0) cc_final: 0.7231 (mt0) REVERT: B 80 LEU cc_start: 0.8172 (mt) cc_final: 0.7948 (tm) REVERT: B 372 PHE cc_start: 0.7597 (m-10) cc_final: 0.7373 (m-10) REVERT: B 457 GLN cc_start: 0.8227 (mt0) cc_final: 0.7954 (mt0) outliers start: 2 outliers final: 1 residues processed: 169 average time/residue: 1.0264 time to fit residues: 184.1456 Evaluate side-chains 89 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 219 ASN B 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7292 Z= 0.202 Angle : 0.661 9.235 9940 Z= 0.332 Chirality : 0.040 0.162 1176 Planarity : 0.005 0.031 1188 Dihedral : 9.106 92.043 1292 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.93 % Favored : 95.62 % Rotamer: Outliers : 2.28 % Allowed : 8.55 % Favored : 89.17 % 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: -2.81 (0.24), residues: 890 helix: -1.49 (0.17), residues: 686 sheet: None (None), residues: 0 loop : -2.56 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 453 HIS 0.002 0.001 HIS B 445 PHE 0.018 0.002 PHE B 194 TYR 0.010 0.002 TYR B 199 ARG 0.004 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.810 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 103 average time/residue: 1.0330 time to fit residues: 113.6060 Evaluate side-chains 77 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.0030 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7292 Z= 0.172 Angle : 0.596 9.153 9940 Z= 0.295 Chirality : 0.039 0.135 1176 Planarity : 0.004 0.033 1188 Dihedral : 7.799 89.482 1290 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.16 % Favored : 95.39 % Rotamer: Outliers : 1.28 % Allowed : 11.68 % Favored : 87.04 % 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: -0.63 (0.28), residues: 890 helix: 0.18 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -2.27 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 445 PHE 0.014 0.001 PHE B 194 TYR 0.009 0.001 TYR B 335 ARG 0.004 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 0.9023 time to fit residues: 90.3667 Evaluate side-chains 81 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7292 Z= 0.156 Angle : 0.559 8.648 9940 Z= 0.276 Chirality : 0.037 0.135 1176 Planarity : 0.003 0.034 1188 Dihedral : 7.181 84.012 1290 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.49 % Favored : 95.06 % Rotamer: Outliers : 1.85 % Allowed : 11.68 % Favored : 86.47 % 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: 0.47 (0.29), residues: 890 helix: 1.02 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.001 0.000 HIS B 445 PHE 0.015 0.001 PHE A 30 TYR 0.010 0.001 TYR B 335 ARG 0.003 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.7932 (OUTLIER) cc_final: 0.7697 (p) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.9571 time to fit residues: 99.6085 Evaluate side-chains 82 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7292 Z= 0.139 Angle : 0.541 8.471 9940 Z= 0.266 Chirality : 0.037 0.132 1176 Planarity : 0.003 0.035 1188 Dihedral : 6.824 82.088 1290 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.27 % Favored : 95.28 % Rotamer: Outliers : 1.85 % Allowed : 11.68 % Favored : 86.47 % 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: 0.96 (0.29), residues: 890 helix: 1.39 (0.21), residues: 688 sheet: None (None), residues: 0 loop : -1.99 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 197 HIS 0.001 0.000 HIS B 445 PHE 0.014 0.001 PHE B 30 TYR 0.010 0.001 TYR B 335 ARG 0.005 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.743 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.8483 time to fit residues: 83.5093 Evaluate side-chains 83 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7292 Z= 0.185 Angle : 0.576 8.508 9940 Z= 0.281 Chirality : 0.038 0.141 1176 Planarity : 0.003 0.035 1188 Dihedral : 6.976 83.583 1290 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.72 % Favored : 94.83 % Rotamer: Outliers : 1.85 % Allowed : 12.54 % Favored : 85.61 % 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: 1.16 (0.29), residues: 890 helix: 1.52 (0.21), residues: 688 sheet: None (None), residues: 0 loop : -1.88 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 445 PHE 0.015 0.001 PHE A 30 TYR 0.009 0.001 TYR A 534 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.9090 time to fit residues: 85.4421 Evaluate side-chains 80 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7292 Z= 0.222 Angle : 0.603 8.367 9940 Z= 0.295 Chirality : 0.040 0.140 1176 Planarity : 0.004 0.058 1188 Dihedral : 7.226 88.320 1290 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 2.28 % Allowed : 12.54 % Favored : 85.19 % 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: 1.19 (0.29), residues: 890 helix: 1.56 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 94 HIS 0.002 0.001 HIS A 348 PHE 0.016 0.002 PHE B 30 TYR 0.009 0.002 TYR A 52 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7871 (tpt) cc_final: 0.7479 (tpt) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.8004 time to fit residues: 82.5639 Evaluate side-chains 80 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.0020 chunk 59 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7292 Z= 0.147 Angle : 0.559 8.126 9940 Z= 0.271 Chirality : 0.038 0.148 1176 Planarity : 0.003 0.052 1188 Dihedral : 6.682 80.013 1290 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.82 % Favored : 95.73 % Rotamer: Outliers : 1.57 % Allowed : 14.10 % Favored : 84.33 % 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: 1.43 (0.29), residues: 890 helix: 1.72 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.73 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 445 PHE 0.014 0.001 PHE A 30 TYR 0.011 0.001 TYR B 335 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.692 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.9413 time to fit residues: 87.9930 Evaluate side-chains 84 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7292 Z= 0.242 Angle : 0.622 8.403 9940 Z= 0.303 Chirality : 0.041 0.171 1176 Planarity : 0.003 0.046 1188 Dihedral : 7.160 87.474 1290 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.38 % Favored : 95.17 % Rotamer: Outliers : 2.14 % Allowed : 13.82 % Favored : 84.05 % 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: 1.34 (0.29), residues: 890 helix: 1.58 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.67 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 94 HIS 0.002 0.001 HIS A 348 PHE 0.014 0.002 PHE B 194 TYR 0.010 0.002 TYR A 52 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7976 (tpt) cc_final: 0.7718 (tpt) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 0.8053 time to fit residues: 72.5323 Evaluate side-chains 82 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7292 Z= 0.180 Angle : 0.589 7.976 9940 Z= 0.284 Chirality : 0.039 0.140 1176 Planarity : 0.003 0.039 1188 Dihedral : 6.781 82.385 1290 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 1.14 % Allowed : 14.25 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.29), residues: 890 helix: 1.70 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.001 0.001 HIS A 362 PHE 0.015 0.001 PHE A 30 TYR 0.011 0.001 TYR B 335 ARG 0.004 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7834 (tpt) cc_final: 0.7562 (tpt) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.8029 time to fit residues: 69.9081 Evaluate side-chains 80 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.0060 chunk 51 optimal weight: 2.9990 overall best weight: 0.3532 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101615 restraints weight = 8281.915| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.94 r_work: 0.3167 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7292 Z= 0.148 Angle : 0.569 8.003 9940 Z= 0.273 Chirality : 0.038 0.142 1176 Planarity : 0.003 0.032 1188 Dihedral : 6.412 76.425 1290 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 1.42 % Allowed : 13.96 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.30), residues: 890 helix: 1.81 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -1.48 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 445 PHE 0.016 0.001 PHE A 30 TYR 0.014 0.001 TYR B 335 ARG 0.003 0.000 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.08 seconds wall clock time: 44 minutes 46.42 seconds (2686.42 seconds total)