Starting phenix.real_space_refine on Wed Feb 12 05:27:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzx_36754/02_2025/8jzx_36754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzx_36754/02_2025/8jzx_36754.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzx_36754/02_2025/8jzx_36754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzx_36754/02_2025/8jzx_36754.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzx_36754/02_2025/8jzx_36754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzx_36754/02_2025/8jzx_36754.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.15, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 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: 2.08 Conformation dependent library (CDL) restraints added in 855.4 milliseconds 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... Secondary structure from input PDB file: 44 helices and 2 sheets defined 81.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 33 through 56 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 57 through 63 Processing helix chain 'A' and resid 70 through 88 removed outlier: 3.568A pdb=" N TYR A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.836A pdb=" N ALA A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.661A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 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 153 through 181 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 186 through 212 removed outlier: 3.649A pdb=" N ALA A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) 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 212 through 220 removed outlier: 3.631A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 244 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 328 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 328 through 348 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 365 through 369 removed outlier: 3.528A pdb=" N TRP A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 370 through 388 removed outlier: 4.607A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) 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 390 through 395 removed outlier: 3.601A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.568A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.511A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.728A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 510 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.689A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) 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 26 Processing helix chain 'B' and resid 33 through 56 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 57 through 63 Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.568A pdb=" N TYR B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 removed outlier: 3.836A pdb=" N ALA B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.661A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 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 153 through 181 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 186 through 212 removed outlier: 3.648A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) 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 212 through 220 removed outlier: 3.631A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 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 328 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 328 through 348 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 365 through 369 removed outlier: 3.528A pdb=" N TRP B 368 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 370 through 388 removed outlier: 4.607A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) 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 390 through 395 removed outlier: 3.600A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 430 removed outlier: 3.568A pdb=" N ARG B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 413 " --> pdb=" O MET B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 removed outlier: 3.511A pdb=" N TRP B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 453' Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.728A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.689A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing sheet with id=AA1, 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=AA2, 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) 481 hydrogen bonds defined for protein. 1437 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: 2.13 Time building geometry restraints manager: 2.25 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 1.464 1.212 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C25 Q09 A 603 " pdb=" N26 Q09 A 603 " ideal model delta sigma weight residual 1.464 1.212 0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C20 Q09 A 603 " pdb=" N22 Q09 A 603 " ideal model delta sigma weight residual 1.343 1.457 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C20 Q09 B 604 " pdb=" N22 Q09 B 604 " ideal model delta sigma weight residual 1.343 1.457 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C28 Q09 B 604 " pdb=" C29 Q09 B 604 " ideal model delta sigma weight residual 1.524 1.442 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 7287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 9507 2.33 - 4.65: 327 4.65 - 6.98: 79 6.98 - 9.31: 21 9.31 - 11.64: 6 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 - 16.73: 4177 16.73 - 33.45: 197 33.45 - 50.18: 30 50.18 - 66.91: 18 66.91 - 83.64: 6 Dihedral angle restraints: 4428 sinusoidal: 1832 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 4425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1058 0.082 - 0.164: 90 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: 2211 2.82 - 3.34: 6508 3.34 - 3.86: 11688 3.86 - 4.38: 14332 4.38 - 4.90: 24430 Nonbonded interactions: 59169 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 3.120 nonbonded pdb=" O ALA B 27 " pdb=" NH1 ARG B 193 " model vdw 2.368 3.120 nonbonded pdb=" O PHE B 30 " pdb=" N GLY B 32 " model vdw 2.385 3.120 ... (remaining 59164 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: 0.04 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: 6.200 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.240 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- 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 : 0.009 0.252 7292 Z= 0.592 Angle : 1.136 11.637 9940 Z= 0.581 Chirality : 0.060 0.409 1176 Planarity : 0.007 0.050 1188 Dihedral : 11.298 83.636 2758 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 to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.776 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: 1.0786 time to fit residues: 193.4821 Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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: 0.2980 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102789 restraints weight = 8256.431| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.93 r_work: 0.3180 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2444 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= 0.181 Angle : 0.694 9.839 9940 Z= 0.356 Chirality : 0.041 0.194 1176 Planarity : 0.005 0.036 1188 Dihedral : 9.603 73.510 1314 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.16 % Favored : 95.39 % Rotamer: Outliers : 1.85 % Allowed : 9.69 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.23), residues: 890 helix: -1.35 (0.16), residues: 698 sheet: None (None), residues: 0 loop : -2.96 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 PHE 0.016 0.002 PHE B 194 TYR 0.008 0.001 TYR B 335 ARG 0.006 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 108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 386 LYS cc_start: 0.8354 (mptp) cc_final: 0.8061 (mmtt) REVERT: A 453 TRP cc_start: 0.7574 (m100) cc_final: 0.7025 (m100) REVERT: A 465 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 84 LEU cc_start: 0.8541 (tp) cc_final: 0.8242 (tp) REVERT: B 151 ARG cc_start: 0.6833 (mtt90) cc_final: 0.6539 (mtp180) REVERT: B 457 GLN cc_start: 0.8053 (mt0) cc_final: 0.7427 (mt0) REVERT: B 482 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8492 (tptt) outliers start: 13 outliers final: 2 residues processed: 102 average time/residue: 1.1513 time to fit residues: 125.9453 Evaluate side-chains 87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 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 457 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.129251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099783 restraints weight = 8310.353| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.96 r_work: 0.3137 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7292 Z= 0.207 Angle : 0.635 9.523 9940 Z= 0.322 Chirality : 0.039 0.140 1176 Planarity : 0.004 0.034 1188 Dihedral : 8.078 59.363 1312 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.94 % Favored : 94.61 % Rotamer: Outliers : 1.28 % Allowed : 11.54 % Favored : 87.18 % 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: -0.13 (0.28), residues: 890 helix: 0.60 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -2.54 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 PHE 0.015 0.002 PHE B 30 TYR 0.011 0.002 TYR A 52 ARG 0.003 0.001 ARG A 394 *********************** 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 109 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.698 Fit side-chains REVERT: A 453 TRP cc_start: 0.8027 (m100) cc_final: 0.7265 (m100) REVERT: B 84 LEU cc_start: 0.8499 (tp) cc_final: 0.8225 (tp) REVERT: B 151 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6456 (mtt90) REVERT: B 184 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8139 (ttpt) REVERT: B 371 MET cc_start: 0.8435 (mtm) cc_final: 0.8199 (mtp) REVERT: B 457 GLN cc_start: 0.8038 (mt0) cc_final: 0.7219 (mt0) REVERT: B 482 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8593 (tptt) REVERT: B 513 LYS cc_start: 0.7373 (ptpp) cc_final: 0.7098 (ttpt) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 1.1172 time to fit residues: 122.1622 Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.124636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095649 restraints weight = 8409.988| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.94 r_work: 0.3079 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7292 Z= 0.278 Angle : 0.681 10.157 9940 Z= 0.340 Chirality : 0.042 0.184 1176 Planarity : 0.004 0.038 1188 Dihedral : 7.867 49.838 1312 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.17 % Favored : 94.38 % Rotamer: Outliers : 2.14 % Allowed : 11.68 % Favored : 86.18 % 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: 0.66 (0.29), residues: 890 helix: 1.20 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.37 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 94 HIS 0.004 0.001 HIS A 348 PHE 0.019 0.002 PHE A 30 TYR 0.009 0.002 TYR A 52 ARG 0.005 0.001 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 103 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8641 (mt0) REVERT: A 373 ASP cc_start: 0.8143 (t0) cc_final: 0.7843 (p0) REVERT: B 151 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6568 (mtt90) REVERT: B 184 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8049 (ttpt) REVERT: B 371 MET cc_start: 0.8528 (mtm) cc_final: 0.8258 (mtp) outliers start: 15 outliers final: 5 residues processed: 96 average time/residue: 1.0831 time to fit residues: 110.6725 Evaluate side-chains 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 319 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 75 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 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: B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097996 restraints weight = 8332.464| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.92 r_work: 0.3113 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7292 Z= 0.197 Angle : 0.628 9.986 9940 Z= 0.312 Chirality : 0.040 0.149 1176 Planarity : 0.004 0.062 1188 Dihedral : 7.353 50.883 1312 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.61 % Favored : 94.94 % Rotamer: Outliers : 1.71 % Allowed : 12.68 % 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: 1.11 (0.29), residues: 890 helix: 1.52 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.29 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS A 348 PHE 0.015 0.001 PHE B 30 TYR 0.010 0.001 TYR A 52 ARG 0.002 0.000 ARG B 404 *********************** 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 97 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 ARG cc_start: 0.7208 (mtt90) cc_final: 0.6697 (mtt90) REVERT: B 371 MET cc_start: 0.8444 (mtm) cc_final: 0.8228 (mtp) outliers start: 12 outliers final: 5 residues processed: 92 average time/residue: 0.9719 time to fit residues: 95.9990 Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU 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 59 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 0.0010 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.129640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101398 restraints weight = 8297.846| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.90 r_work: 0.3166 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7292 Z= 0.162 Angle : 0.595 9.450 9940 Z= 0.296 Chirality : 0.038 0.131 1176 Planarity : 0.004 0.056 1188 Dihedral : 6.828 50.794 1312 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.61 % Favored : 94.94 % Rotamer: Outliers : 1.71 % Allowed : 13.11 % 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: 1.51 (0.29), residues: 890 helix: 1.82 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.25 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 197 HIS 0.002 0.000 HIS A 348 PHE 0.014 0.001 PHE A 30 TYR 0.010 0.001 TYR B 335 ARG 0.002 0.000 ARG A 394 *********************** 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 98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8085 (m-80) cc_final: 0.7672 (m-80) REVERT: B 84 LEU cc_start: 0.8509 (tp) cc_final: 0.8219 (tp) REVERT: B 151 ARG cc_start: 0.7206 (mtt90) cc_final: 0.6672 (mtt90) REVERT: B 457 GLN cc_start: 0.7782 (mt0) cc_final: 0.7185 (mt0) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.9291 time to fit residues: 94.1679 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.127065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098455 restraints weight = 8315.018| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.90 r_work: 0.3120 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7292 Z= 0.200 Angle : 0.624 9.984 9940 Z= 0.308 Chirality : 0.039 0.133 1176 Planarity : 0.004 0.055 1188 Dihedral : 6.897 49.939 1312 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 1.71 % Allowed : 13.53 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 890 helix: 1.89 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.12 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 PHE 0.015 0.001 PHE B 120 TYR 0.011 0.001 TYR A 113 ARG 0.002 0.000 ARG B 404 *********************** 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 94 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8134 (m-80) cc_final: 0.7745 (m-80) REVERT: B 84 LEU cc_start: 0.8502 (tp) cc_final: 0.8222 (tp) REVERT: B 151 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6617 (mtt90) REVERT: B 453 TRP cc_start: 0.7911 (m100) cc_final: 0.7669 (m100) REVERT: B 457 GLN cc_start: 0.7901 (mt0) cc_final: 0.7241 (mt0) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.9051 time to fit residues: 88.7705 Evaluate side-chains 87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098168 restraints weight = 8367.661| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.93 r_work: 0.3118 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7292 Z= 0.207 Angle : 0.632 9.483 9940 Z= 0.311 Chirality : 0.040 0.146 1176 Planarity : 0.004 0.052 1188 Dihedral : 6.870 50.115 1312 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.27 % Favored : 95.28 % Rotamer: Outliers : 1.71 % Allowed : 13.82 % Favored : 84.47 % 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: 1.68 (0.29), residues: 890 helix: 1.86 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.97 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 PHE 0.021 0.001 PHE B 120 TYR 0.011 0.001 TYR A 52 ARG 0.002 0.000 ARG A 404 *********************** 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 91 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7838 (tpt) cc_final: 0.7469 (tpt) REVERT: B 151 ARG cc_start: 0.7135 (mtt90) cc_final: 0.6544 (mtt90) REVERT: B 453 TRP cc_start: 0.7901 (m100) cc_final: 0.7678 (m100) REVERT: B 457 GLN cc_start: 0.7911 (mt0) cc_final: 0.7253 (mt0) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.9988 time to fit residues: 94.3920 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU 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 66 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.127169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098325 restraints weight = 8404.117| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.93 r_work: 0.3121 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7292 Z= 0.195 Angle : 0.627 9.153 9940 Z= 0.309 Chirality : 0.040 0.144 1176 Planarity : 0.004 0.049 1188 Dihedral : 6.756 49.389 1312 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.27 % Favored : 95.28 % Rotamer: Outliers : 1.71 % Allowed : 14.10 % Favored : 84.19 % 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: 1.76 (0.29), residues: 890 helix: 1.91 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.91 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 PHE 0.020 0.001 PHE B 120 TYR 0.011 0.001 TYR A 52 ARG 0.002 0.000 ARG A 193 *********************** 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 93 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8143 (m-80) cc_final: 0.7740 (m-80) REVERT: B 151 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6720 (mtt90) REVERT: B 457 GLN cc_start: 0.7909 (mt0) cc_final: 0.7234 (mt0) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.9488 time to fit residues: 89.5923 Evaluate side-chains 87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 A residue 464 SER Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU 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 89 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.127986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099573 restraints weight = 8470.268| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.92 r_work: 0.3137 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7292 Z= 0.181 Angle : 0.624 9.116 9940 Z= 0.306 Chirality : 0.039 0.143 1176 Planarity : 0.004 0.046 1188 Dihedral : 6.577 49.816 1312 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 1.28 % Allowed : 14.53 % Favored : 84.19 % 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: 1.86 (0.29), residues: 890 helix: 1.99 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.92 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 PHE 0.019 0.001 PHE B 120 TYR 0.012 0.001 TYR B 335 ARG 0.003 0.000 ARG A 193 ********************** 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 88 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8132 (m-80) cc_final: 0.7700 (m-80) REVERT: B 151 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6706 (mtt90) REVERT: B 457 GLN cc_start: 0.7891 (mt0) cc_final: 0.7142 (mt0) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.9906 time to fit residues: 90.2458 Evaluate side-chains 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 A residue 464 SER Chi-restraints excluded: chain B residue 79 LEU 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 15 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.128476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099936 restraints weight = 8338.299| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.92 r_work: 0.3142 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7292 Z= 0.179 Angle : 0.620 8.852 9940 Z= 0.305 Chirality : 0.039 0.145 1176 Planarity : 0.004 0.039 1188 Dihedral : 6.466 49.655 1312 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.38 % Favored : 95.17 % Rotamer: Outliers : 1.42 % Allowed : 14.10 % Favored : 84.47 % 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: 1.89 (0.29), residues: 890 helix: 2.01 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.90 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 PHE 0.018 0.001 PHE B 120 TYR 0.013 0.001 TYR B 335 ARG 0.004 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4872.69 seconds wall clock time: 87 minutes 17.70 seconds (5237.70 seconds total)