Starting phenix.real_space_refine on Sat Sep 28 19:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/09_2024/6u8a_20686.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/09_2024/6u8a_20686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/09_2024/6u8a_20686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/09_2024/6u8a_20686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/09_2024/6u8a_20686.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/09_2024/6u8a_20686.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13172 2.51 5 N 3324 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 12.94, per 1000 atoms: 0.65 Number of scatterers: 20032 At special positions: 0 Unit cell: (126.14, 126.14, 111.3, 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 116 16.00 O 3420 8.00 N 3324 7.00 C 13172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.5 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 61.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.619A pdb=" N THR C 112 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.037A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.329A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.837A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.705A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.623A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 6.661A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 6.659A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3108 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: 6.03 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5115 1.46 - 1.58: 9112 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 20544 Sorted by residual: bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T A1002 " pdb=" O02 P0T A1002 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T D1001 " pdb=" O02 P0T D1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C11 P0T A1001 " pdb=" O01 P0T A1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 20539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 26945 2.34 - 4.67: 796 4.67 - 7.01: 83 7.01 - 9.34: 36 9.34 - 11.68: 16 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ILE D 529 " pdb=" CA ILE D 529 " pdb=" C ILE D 529 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N ILE B 529 " pdb=" CA ILE B 529 " pdb=" C ILE B 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.83e+01 angle pdb=" N ILE C 529 " pdb=" CA ILE C 529 " pdb=" C ILE C 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 122.80 -11.68 3.00e+00 1.11e-01 1.52e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 10837 19.27 - 38.53: 1023 38.53 - 57.80: 196 57.80 - 77.07: 32 77.07 - 96.33: 12 Dihedral angle restraints: 12100 sinusoidal: 4880 harmonic: 7220 Sorted by residual: dihedral pdb=" CA ASN C 655 " pdb=" C ASN C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 655 " pdb=" C ASN A 655 " pdb=" N SER A 656 " pdb=" CA SER A 656 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN B 655 " pdb=" C ASN B 655 " pdb=" N SER B 656 " pdb=" CA SER B 656 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1999 0.045 - 0.090: 861 0.090 - 0.135: 212 0.135 - 0.180: 68 0.180 - 0.225: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C03 P0T A1002 " pdb=" C04 P0T A1002 " pdb=" C05 P0T A1002 " pdb=" C10 P0T A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T C1001 " pdb=" C04 P0T C1001 " pdb=" C05 P0T C1001 " pdb=" C10 P0T C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C05 P0T A1001 " pdb=" C10 P0T A1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3145 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO D 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6104 2.82 - 3.34: 17959 3.34 - 3.86: 33559 3.86 - 4.38: 37894 4.38 - 4.90: 66133 Nonbonded interactions: 161649 Sorted by model distance: nonbonded pdb=" O GLU C 90 " pdb=" OG1 THR C 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU D 90 " pdb=" OG1 THR D 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU A 90 " pdb=" OG1 THR A 93 " model vdw 2.297 3.040 nonbonded pdb=" O GLU B 90 " pdb=" OG1 THR B 93 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.302 3.120 ... (remaining 161644 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 719) selection = chain 'B' selection = (chain 'C' and resid 32 through 719) selection = (chain 'D' and resid 32 through 719) } 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: 1.200 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 44.390 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.050 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 0.065 20544 Z= 0.513 Angle : 0.966 11.681 27876 Z= 0.497 Chirality : 0.054 0.225 3148 Planarity : 0.007 0.067 3420 Dihedral : 15.898 96.335 7428 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.37 % Allowed : 8.94 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.94 (0.12), residues: 2428 helix: -2.38 (0.09), residues: 1460 sheet: -2.79 (0.43), residues: 92 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS D 251 PHE 0.019 0.003 PHE B 161 TYR 0.013 0.002 TYR D 111 ARG 0.004 0.001 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 405 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7255 (mm) cc_final: 0.6674 (pp) REVERT: A 113 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 173 GLU cc_start: 0.8400 (tp30) cc_final: 0.8198 (tp30) REVERT: A 541 LEU cc_start: 0.9104 (tp) cc_final: 0.8896 (tp) REVERT: B 255 MET cc_start: 0.8120 (mmm) cc_final: 0.7902 (mmm) REVERT: B 372 MET cc_start: 0.9125 (mtt) cc_final: 0.8903 (mtt) REVERT: B 383 GLN cc_start: 0.7898 (tp40) cc_final: 0.7604 (tt0) REVERT: B 404 MET cc_start: 0.8670 (mmp) cc_final: 0.8460 (mmt) REVERT: B 541 LEU cc_start: 0.9052 (tp) cc_final: 0.8787 (tp) REVERT: B 640 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttp) REVERT: C 113 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7058 (mt-10) REVERT: C 235 GLN cc_start: 0.7661 (mt0) cc_final: 0.7435 (mt0) REVERT: C 255 MET cc_start: 0.8176 (mmm) cc_final: 0.7930 (mmt) REVERT: C 464 TRP cc_start: 0.6065 (m100) cc_final: 0.5829 (m100) REVERT: D 113 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7088 (mt-10) REVERT: D 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7959 (mmt) REVERT: D 305 GLU cc_start: 0.7603 (tt0) cc_final: 0.7064 (mt-10) REVERT: D 464 TRP cc_start: 0.6079 (m100) cc_final: 0.5860 (m100) REVERT: D 473 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7529 (mp0) REVERT: D 528 MET cc_start: 0.8073 (ttt) cc_final: 0.7569 (ttt) REVERT: D 536 ASP cc_start: 0.7392 (t70) cc_final: 0.7190 (t0) outliers start: 8 outliers final: 0 residues processed: 405 average time/residue: 0.2976 time to fit residues: 187.6307 Evaluate side-chains 270 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 316 GLN A 414 GLN A 487 GLN B 163 GLN B 186 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 316 GLN C 186 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 316 GLN D 186 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 316 GLN D 487 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20544 Z= 0.174 Angle : 0.527 7.673 27876 Z= 0.268 Chirality : 0.037 0.191 3148 Planarity : 0.005 0.063 3420 Dihedral : 6.981 54.962 2772 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.91 % Allowed : 13.55 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.27 (0.16), residues: 2428 helix: -0.03 (0.12), residues: 1476 sheet: -2.14 (0.47), residues: 92 loop : -2.03 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 715 HIS 0.005 0.001 HIS B 251 PHE 0.017 0.001 PHE D 467 TYR 0.016 0.001 TYR D 455 ARG 0.005 0.000 ARG B 706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 353 time to evaluate : 2.285 Fit side-chains REVERT: A 92 LEU cc_start: 0.7181 (mm) cc_final: 0.6433 (pp) REVERT: A 536 ASP cc_start: 0.7302 (t70) cc_final: 0.7098 (t0) REVERT: B 383 GLN cc_start: 0.7949 (tp40) cc_final: 0.7702 (tp40) REVERT: B 645 MET cc_start: 0.7677 (tmm) cc_final: 0.7147 (tmm) REVERT: C 111 TYR cc_start: 0.5880 (m-80) cc_final: 0.5511 (m-80) REVERT: C 118 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8167 (tttt) REVERT: C 305 GLU cc_start: 0.7548 (tt0) cc_final: 0.7230 (mt-10) REVERT: D 111 TYR cc_start: 0.5751 (m-80) cc_final: 0.5462 (m-80) REVERT: D 118 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8114 (tttt) REVERT: D 255 MET cc_start: 0.8306 (mmm) cc_final: 0.7907 (mmt) REVERT: D 305 GLU cc_start: 0.7526 (tt0) cc_final: 0.6907 (mt-10) REVERT: D 446 ILE cc_start: 0.9079 (tp) cc_final: 0.8814 (tp) outliers start: 41 outliers final: 21 residues processed: 382 average time/residue: 0.2760 time to fit residues: 168.3960 Evaluate side-chains 297 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 276 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 316 GLN Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 0.0170 chunk 61 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 487 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 487 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20544 Z= 0.182 Angle : 0.531 10.108 27876 Z= 0.260 Chirality : 0.036 0.197 3148 Planarity : 0.004 0.058 3420 Dihedral : 6.670 58.158 2772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.49 % Allowed : 16.34 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.17), residues: 2428 helix: 0.94 (0.13), residues: 1456 sheet: -1.75 (0.48), residues: 92 loop : -1.65 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 715 HIS 0.005 0.001 HIS B 313 PHE 0.017 0.001 PHE B 405 TYR 0.012 0.001 TYR D 455 ARG 0.004 0.000 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 306 time to evaluate : 2.355 Fit side-chains REVERT: A 92 LEU cc_start: 0.7222 (mm) cc_final: 0.6346 (pp) REVERT: A 269 HIS cc_start: 0.7370 (t70) cc_final: 0.7117 (t70) REVERT: A 536 ASP cc_start: 0.7442 (t70) cc_final: 0.7216 (t0) REVERT: B 383 GLN cc_start: 0.7923 (tp40) cc_final: 0.7603 (tt0) REVERT: B 645 MET cc_start: 0.7788 (tmm) cc_final: 0.6994 (tmm) REVERT: C 111 TYR cc_start: 0.5789 (m-80) cc_final: 0.5418 (m-80) REVERT: C 118 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8168 (ttpt) REVERT: C 305 GLU cc_start: 0.7542 (tt0) cc_final: 0.7140 (mt-10) REVERT: C 379 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7956 (t0) REVERT: D 111 TYR cc_start: 0.5824 (m-80) cc_final: 0.5512 (m-80) REVERT: D 118 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8256 (ttpt) REVERT: D 255 MET cc_start: 0.8281 (mmm) cc_final: 0.7839 (mmt) REVERT: D 305 GLU cc_start: 0.7562 (tt0) cc_final: 0.6917 (mt-10) REVERT: D 446 ILE cc_start: 0.9069 (tp) cc_final: 0.8799 (tp) outliers start: 32 outliers final: 17 residues processed: 329 average time/residue: 0.2767 time to fit residues: 146.0188 Evaluate side-chains 289 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20544 Z= 0.148 Angle : 0.496 8.322 27876 Z= 0.246 Chirality : 0.036 0.175 3148 Planarity : 0.004 0.055 3420 Dihedral : 6.233 59.917 2772 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.56 % Allowed : 16.39 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.17), residues: 2428 helix: 1.43 (0.14), residues: 1472 sheet: -1.57 (0.50), residues: 92 loop : -1.45 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 715 HIS 0.008 0.001 HIS A 313 PHE 0.019 0.001 PHE A 467 TYR 0.013 0.001 TYR C 455 ARG 0.003 0.000 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 317 time to evaluate : 2.300 Fit side-chains REVERT: A 39 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6008 (p90) REVERT: A 92 LEU cc_start: 0.6992 (mm) cc_final: 0.6193 (pp) REVERT: A 269 HIS cc_start: 0.7493 (t70) cc_final: 0.7265 (t70) REVERT: A 536 ASP cc_start: 0.7241 (t70) cc_final: 0.7028 (t0) REVERT: A 670 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7137 (tt0) REVERT: B 39 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5963 (p90) REVERT: B 383 GLN cc_start: 0.7810 (tp40) cc_final: 0.7572 (tt0) REVERT: B 634 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: B 689 LEU cc_start: 0.7771 (mt) cc_final: 0.7569 (mp) REVERT: C 111 TYR cc_start: 0.5435 (m-80) cc_final: 0.5172 (m-80) REVERT: C 305 GLU cc_start: 0.7389 (tt0) cc_final: 0.7020 (mt-10) REVERT: C 379 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8010 (t0) REVERT: C 634 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: D 235 GLN cc_start: 0.7548 (mt0) cc_final: 0.7317 (mt0) REVERT: D 670 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7070 (tp30) outliers start: 55 outliers final: 27 residues processed: 359 average time/residue: 0.2741 time to fit residues: 156.0433 Evaluate side-chains 303 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 271 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS B 127 ASN B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20544 Z= 0.298 Angle : 0.583 9.896 27876 Z= 0.286 Chirality : 0.039 0.179 3148 Planarity : 0.004 0.050 3420 Dihedral : 7.071 61.465 2772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.89 % Allowed : 17.41 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.38 (0.17), residues: 2428 helix: 1.35 (0.13), residues: 1500 sheet: -1.61 (0.50), residues: 92 loop : -1.59 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 333 HIS 0.005 0.001 HIS B 313 PHE 0.019 0.002 PHE B 405 TYR 0.011 0.002 TYR B 455 ARG 0.004 0.000 ARG D 591 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 267 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.5795 (p90) REVERT: A 92 LEU cc_start: 0.7251 (mm) cc_final: 0.6399 (pp) REVERT: A 670 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7127 (tp30) REVERT: B 39 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.5935 (p90) REVERT: B 473 GLU cc_start: 0.7791 (mp0) cc_final: 0.7517 (mm-30) REVERT: C 39 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.5901 (p90) REVERT: C 473 GLU cc_start: 0.7790 (mp0) cc_final: 0.7581 (mm-30) REVERT: C 634 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: C 670 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7148 (tp30) REVERT: D 39 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.5616 (p90) REVERT: D 92 LEU cc_start: 0.7619 (mt) cc_final: 0.7211 (mt) REVERT: D 473 GLU cc_start: 0.7801 (mp0) cc_final: 0.7586 (mm-30) REVERT: D 670 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7161 (tp30) outliers start: 62 outliers final: 30 residues processed: 307 average time/residue: 0.2967 time to fit residues: 143.8946 Evaluate side-chains 286 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20544 Z= 0.151 Angle : 0.500 7.728 27876 Z= 0.248 Chirality : 0.036 0.155 3148 Planarity : 0.004 0.048 3420 Dihedral : 6.305 58.082 2772 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.61 % Allowed : 18.25 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.88 (0.17), residues: 2428 helix: 1.84 (0.14), residues: 1456 sheet: -1.58 (0.51), residues: 92 loop : -1.36 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 715 HIS 0.007 0.001 HIS A 313 PHE 0.021 0.001 PHE B 467 TYR 0.012 0.001 TYR C 455 ARG 0.006 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.5693 (p90) REVERT: A 92 LEU cc_start: 0.7084 (mm) cc_final: 0.6312 (pp) REVERT: B 39 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.5753 (p90) REVERT: B 545 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9197 (mt) REVERT: B 634 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: C 39 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.5682 (p90) REVERT: C 92 LEU cc_start: 0.7625 (mt) cc_final: 0.7270 (mt) REVERT: C 379 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7909 (t0) REVERT: C 634 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: D 39 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.5692 (p90) REVERT: D 92 LEU cc_start: 0.7699 (mt) cc_final: 0.6286 (pp) REVERT: D 473 GLU cc_start: 0.7783 (mp0) cc_final: 0.7547 (mm-30) REVERT: D 670 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7101 (tp30) outliers start: 56 outliers final: 28 residues processed: 342 average time/residue: 0.2778 time to fit residues: 153.9644 Evaluate side-chains 304 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 0.3980 chunk 235 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20544 Z= 0.148 Angle : 0.512 11.810 27876 Z= 0.248 Chirality : 0.036 0.176 3148 Planarity : 0.003 0.048 3420 Dihedral : 5.873 52.196 2772 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.47 % Allowed : 19.18 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.18), residues: 2428 helix: 2.01 (0.14), residues: 1456 sheet: -1.53 (0.50), residues: 92 loop : -1.24 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 715 HIS 0.007 0.001 HIS B 313 PHE 0.023 0.001 PHE B 467 TYR 0.012 0.001 TYR B 455 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 291 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5683 (p90) REVERT: A 92 LEU cc_start: 0.6725 (mm) cc_final: 0.6029 (pp) REVERT: A 528 MET cc_start: 0.8203 (ptm) cc_final: 0.7893 (ttp) REVERT: B 39 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5737 (p90) REVERT: B 473 GLU cc_start: 0.7679 (mp0) cc_final: 0.7408 (mm-30) REVERT: B 492 MET cc_start: 0.6600 (ttt) cc_final: 0.6364 (ttt) REVERT: C 39 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.5583 (p90) REVERT: C 92 LEU cc_start: 0.7538 (mt) cc_final: 0.6204 (pp) REVERT: C 379 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7904 (t0) REVERT: C 473 GLU cc_start: 0.7725 (mp0) cc_final: 0.7458 (mm-30) REVERT: C 528 MET cc_start: 0.8162 (ptm) cc_final: 0.7802 (ttp) REVERT: C 634 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: D 39 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5617 (p90) REVERT: D 92 LEU cc_start: 0.7632 (mt) cc_final: 0.6207 (pp) REVERT: D 235 GLN cc_start: 0.7575 (mt0) cc_final: 0.7344 (mt0) REVERT: D 473 GLU cc_start: 0.7701 (mp0) cc_final: 0.7440 (mm-30) outliers start: 53 outliers final: 34 residues processed: 323 average time/residue: 0.2827 time to fit residues: 144.8709 Evaluate side-chains 300 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 70 optimal weight: 0.0060 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20544 Z= 0.183 Angle : 0.535 12.126 27876 Z= 0.259 Chirality : 0.037 0.197 3148 Planarity : 0.003 0.045 3420 Dihedral : 5.870 52.316 2772 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.65 % Allowed : 19.09 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.14 (0.18), residues: 2428 helix: 2.02 (0.14), residues: 1456 sheet: -1.58 (0.50), residues: 92 loop : -1.18 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 715 HIS 0.006 0.001 HIS A 269 PHE 0.023 0.001 PHE C 467 TYR 0.013 0.001 TYR B 544 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 270 time to evaluate : 2.426 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5675 (p90) REVERT: A 92 LEU cc_start: 0.6862 (mm) cc_final: 0.6178 (pp) REVERT: A 473 GLU cc_start: 0.7709 (mp0) cc_final: 0.7408 (mm-30) REVERT: A 528 MET cc_start: 0.8191 (ptm) cc_final: 0.7900 (ttp) REVERT: A 634 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: B 39 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.5695 (p90) REVERT: B 92 LEU cc_start: 0.7554 (mt) cc_final: 0.7184 (mt) REVERT: B 473 GLU cc_start: 0.7683 (mp0) cc_final: 0.7415 (mm-30) REVERT: B 634 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: C 39 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.5631 (p90) REVERT: C 92 LEU cc_start: 0.7616 (mt) cc_final: 0.6284 (pp) REVERT: C 473 GLU cc_start: 0.7718 (mp0) cc_final: 0.7493 (mm-30) REVERT: C 528 MET cc_start: 0.8193 (ptm) cc_final: 0.7852 (ttp) REVERT: C 634 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: C 670 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7142 (tp30) REVERT: D 39 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.5571 (p90) REVERT: D 92 LEU cc_start: 0.7666 (mt) cc_final: 0.6230 (pp) REVERT: D 473 GLU cc_start: 0.7718 (mp0) cc_final: 0.7456 (mm-30) outliers start: 57 outliers final: 33 residues processed: 305 average time/residue: 0.3160 time to fit residues: 155.2287 Evaluate side-chains 294 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 254 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.0070 chunk 225 optimal weight: 0.4980 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 20544 Z= 0.156 Angle : 0.517 11.433 27876 Z= 0.251 Chirality : 0.037 0.223 3148 Planarity : 0.003 0.045 3420 Dihedral : 5.556 51.406 2772 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.23 % Allowed : 19.51 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.26 (0.18), residues: 2428 helix: 2.09 (0.14), residues: 1456 sheet: -1.53 (0.50), residues: 92 loop : -1.11 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 715 HIS 0.005 0.001 HIS D 269 PHE 0.025 0.001 PHE B 467 TYR 0.012 0.001 TYR B 455 ARG 0.007 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 2.255 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5718 (p90) REVERT: A 92 LEU cc_start: 0.6807 (mm) cc_final: 0.6153 (pp) REVERT: A 473 GLU cc_start: 0.7677 (mp0) cc_final: 0.7397 (mm-30) REVERT: A 528 MET cc_start: 0.8135 (ptm) cc_final: 0.7844 (ttp) REVERT: A 634 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: B 39 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5727 (p90) REVERT: B 92 LEU cc_start: 0.7397 (mt) cc_final: 0.7038 (mt) REVERT: B 473 GLU cc_start: 0.7631 (mp0) cc_final: 0.7352 (mm-30) REVERT: B 634 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: C 39 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.5527 (p90) REVERT: C 92 LEU cc_start: 0.7552 (mt) cc_final: 0.6225 (pp) REVERT: C 379 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7893 (t0) REVERT: C 473 GLU cc_start: 0.7648 (mp0) cc_final: 0.7387 (mm-30) REVERT: C 528 MET cc_start: 0.8154 (ptm) cc_final: 0.7812 (ttp) REVERT: C 634 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: D 39 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5565 (p90) REVERT: D 92 LEU cc_start: 0.7552 (mt) cc_final: 0.6176 (pp) REVERT: D 235 GLN cc_start: 0.7692 (mt0) cc_final: 0.7383 (mt0) REVERT: D 473 GLU cc_start: 0.7686 (mp0) cc_final: 0.7431 (mm-30) outliers start: 48 outliers final: 33 residues processed: 314 average time/residue: 0.2787 time to fit residues: 140.1055 Evaluate side-chains 299 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 0.0670 chunk 243 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20544 Z= 0.149 Angle : 0.522 10.560 27876 Z= 0.252 Chirality : 0.036 0.151 3148 Planarity : 0.003 0.046 3420 Dihedral : 5.350 53.030 2772 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.14 % Allowed : 19.93 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2428 helix: 2.18 (0.14), residues: 1456 sheet: -2.36 (0.44), residues: 112 loop : -0.96 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 715 HIS 0.005 0.001 HIS D 269 PHE 0.026 0.001 PHE D 467 TYR 0.012 0.001 TYR D 455 ARG 0.007 0.000 ARG C 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 274 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.5592 (p90) REVERT: A 92 LEU cc_start: 0.6725 (mm) cc_final: 0.6142 (pp) REVERT: A 163 GLN cc_start: 0.8016 (tt0) cc_final: 0.7429 (tp40) REVERT: A 473 GLU cc_start: 0.7727 (mp0) cc_final: 0.7449 (mm-30) REVERT: A 634 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: B 39 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.5610 (p90) REVERT: B 92 LEU cc_start: 0.7389 (mt) cc_final: 0.7028 (mt) REVERT: B 473 GLU cc_start: 0.7672 (mp0) cc_final: 0.7387 (mm-30) REVERT: B 634 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: C 39 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.5592 (p90) REVERT: C 92 LEU cc_start: 0.7544 (mt) cc_final: 0.7163 (mt) REVERT: C 379 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7909 (t0) REVERT: C 473 GLU cc_start: 0.7673 (mp0) cc_final: 0.7413 (mm-30) REVERT: C 528 MET cc_start: 0.8142 (ptm) cc_final: 0.7784 (ttp) REVERT: C 634 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: D 39 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.5591 (p90) REVERT: D 92 LEU cc_start: 0.7548 (mt) cc_final: 0.6206 (pp) REVERT: D 235 GLN cc_start: 0.7590 (mt0) cc_final: 0.7382 (mt0) REVERT: D 473 GLU cc_start: 0.7686 (mp0) cc_final: 0.7423 (mm-30) REVERT: D 634 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6832 (m-80) outliers start: 46 outliers final: 29 residues processed: 302 average time/residue: 0.2752 time to fit residues: 133.6894 Evaluate side-chains 302 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 178 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 overall best weight: 0.5628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128673 restraints weight = 26998.489| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.82 r_work: 0.3314 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20544 Z= 0.144 Angle : 0.518 10.835 27876 Z= 0.250 Chirality : 0.036 0.145 3148 Planarity : 0.003 0.045 3420 Dihedral : 5.206 53.587 2772 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.96 % Allowed : 20.34 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.40 (0.18), residues: 2428 helix: 2.23 (0.14), residues: 1456 sheet: -2.31 (0.44), residues: 112 loop : -0.93 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 715 HIS 0.006 0.001 HIS D 269 PHE 0.025 0.001 PHE B 467 TYR 0.013 0.001 TYR B 455 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.66 seconds wall clock time: 72 minutes 16.12 seconds (4336.12 seconds total)