Starting phenix.real_space_refine on Sat Mar 16 04:15:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho9_34923/03_2024/8ho9_34923_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho9_34923/03_2024/8ho9_34923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho9_34923/03_2024/8ho9_34923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho9_34923/03_2024/8ho9_34923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho9_34923/03_2024/8ho9_34923_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ho9_34923/03_2024/8ho9_34923_neut.pdb" } resolution = 2.25 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 8402 2.51 5 N 2190 2.21 5 O 2839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13463 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "B" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Classifications: {'water': 169} Link IDs: {None: 168} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Time building chain proxies: 6.70, per 1000 atoms: 0.50 Number of scatterers: 13463 At special positions: 0 Unit cell: (133.63, 102.09, 97.94, 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 32 16.00 O 2839 8.00 N 2190 7.00 C 8402 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.81 Conformation dependent library (CDL) restraints added in 2.2 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 26 sheets defined 33.7% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.821A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.616A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.678A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.928A pdb=" N TRP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.725A pdb=" N ILE A 437 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.939A pdb=" N VAL A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.079A pdb=" N LYS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.608A pdb=" N GLY A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.411A pdb=" N ILE A 638 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 641 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.828A pdb=" N TRP A 658 " --> pdb=" O HIS A 654 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.898A pdb=" N ILE A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 686 removed outlier: 3.734A pdb=" N GLU A 685 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP A 686 " --> pdb=" O TYR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.918A pdb=" N TRP A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.871A pdb=" N PHE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 314 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.619A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.686A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 3.916A pdb=" N TRP B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.670A pdb=" N ILE B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.943A pdb=" N VAL B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.016A pdb=" N LYS B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.609A pdb=" N GLY B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 615 Processing helix chain 'B' and resid 635 through 641 removed outlier: 4.378A pdb=" N ILE B 638 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 641 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.823A pdb=" N TRP B 658 " --> pdb=" O HIS B 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.968A pdb=" N ILE B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 removed outlier: 3.710A pdb=" N GLU B 685 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP B 686 " --> pdb=" O TYR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 720 through 732 removed outlier: 3.803A pdb=" N TRP B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.681A pdb=" N SER A 95 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.479A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.479A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER A 208 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER A 244 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A 206 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.897A pdb=" N VAL A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 444 removed outlier: 4.151A pdb=" N PHE A 444 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS A 450 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AB2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.728A pdb=" N ALA A 699 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 716 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.916A pdb=" N LEU A 743 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.675A pdb=" N SER B 95 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.459A pdb=" N ILE B 56 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.459A pdb=" N ILE B 56 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 245 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 208 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER B 244 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B 206 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.909A pdb=" N VAL B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 316 through 319 removed outlier: 6.598A pdb=" N THR B 766 " --> pdb=" O HIS B 805 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 807 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU B 768 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL B 809 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR B 770 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N MET B 811 " --> pdb=" O THR B 770 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS B 772 " --> pdb=" O MET B 811 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AC3, first strand: chain 'B' and resid 441 through 444 removed outlier: 4.145A pdb=" N PHE B 444 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS B 450 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC5, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.688A pdb=" N ALA B 699 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER B 716 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 736 through 739 removed outlier: 3.963A pdb=" N LEU B 743 " --> pdb=" O LEU B 796 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1605 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: 5.38 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 0.96: 4 0.96 - 1.17: 0 1.17 - 1.39: 5586 1.39 - 1.60: 7808 1.60 - 1.81: 64 Bond restraints: 13462 Sorted by residual: bond pdb=" C LYS B 3 " pdb=" O LYS B 3 " ideal model delta sigma weight residual 1.235 0.746 0.489 1.28e-02 6.10e+03 1.46e+03 bond pdb=" C LYS A 3 " pdb=" O LYS A 3 " ideal model delta sigma weight residual 1.235 0.746 0.489 1.28e-02 6.10e+03 1.46e+03 bond pdb=" C GLY A 2 " pdb=" O GLY A 2 " ideal model delta sigma weight residual 1.231 0.870 0.361 2.00e-02 2.50e+03 3.26e+02 bond pdb=" C GLY B 2 " pdb=" O GLY B 2 " ideal model delta sigma weight residual 1.231 0.870 0.361 2.00e-02 2.50e+03 3.26e+02 bond pdb=" CA GLY B 2 " pdb=" C GLY B 2 " ideal model delta sigma weight residual 1.516 1.298 0.218 1.80e-02 3.09e+03 1.47e+02 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.01: 347 107.01 - 113.76: 7003 113.76 - 120.52: 5425 120.52 - 127.27: 5272 127.27 - 134.03: 159 Bond angle restraints: 18206 Sorted by residual: angle pdb=" C LYS B 3 " pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " ideal model delta sigma weight residual 109.37 129.86 -20.49 1.91e+00 2.74e-01 1.15e+02 angle pdb=" C LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta sigma weight residual 109.37 129.84 -20.47 1.91e+00 2.74e-01 1.15e+02 angle pdb=" CA GLY B 2 " pdb=" C GLY B 2 " pdb=" O GLY B 2 " ideal model delta sigma weight residual 120.80 103.91 16.89 2.10e+00 2.27e-01 6.47e+01 angle pdb=" CA GLY A 2 " pdb=" C GLY A 2 " pdb=" O GLY A 2 " ideal model delta sigma weight residual 120.80 103.97 16.83 2.10e+00 2.27e-01 6.42e+01 angle pdb=" N PHE A 4 " pdb=" CA PHE A 4 " pdb=" C PHE A 4 " ideal model delta sigma weight residual 112.30 101.99 10.31 1.36e+00 5.41e-01 5.74e+01 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6833 17.68 - 35.36: 761 35.36 - 53.05: 217 53.05 - 70.73: 51 70.73 - 88.41: 30 Dihedral angle restraints: 7892 sinusoidal: 3192 harmonic: 4700 Sorted by residual: dihedral pdb=" C LYS A 3 " pdb=" N LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta harmonic sigma weight residual -122.60 -147.11 24.51 0 2.50e+00 1.60e-01 9.61e+01 dihedral pdb=" C LYS B 3 " pdb=" N LYS B 3 " pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " ideal model delta harmonic sigma weight residual -122.60 -147.09 24.49 0 2.50e+00 1.60e-01 9.60e+01 dihedral pdb=" N LYS A 3 " pdb=" C LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta harmonic sigma weight residual 122.80 137.19 -14.39 0 2.50e+00 1.60e-01 3.31e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 1854 0.276 - 0.551: 1 0.551 - 0.827: 0 0.827 - 1.103: 2 1.103 - 1.378: 1 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CB THR B 503 " pdb=" CA THR B 503 " pdb=" OG1 THR B 503 " pdb=" CG2 THR B 503 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CA LYS B 3 " pdb=" N LYS B 3 " pdb=" C LYS B 3 " pdb=" CB LYS B 3 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA LYS A 3 " pdb=" N LYS A 3 " pdb=" C LYS A 3 " pdb=" CB LYS A 3 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 1855 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 2 " 0.014 2.00e-02 2.50e+03 3.09e-02 9.55e+00 pdb=" C GLY B 2 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B 2 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 3 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 2 " -0.014 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLY A 2 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 2 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 3 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 680 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 681 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 681 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 681 " 0.026 5.00e-02 4.00e+02 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 141 2.54 - 3.13: 10153 3.13 - 3.72: 22474 3.72 - 4.31: 36713 4.31 - 4.90: 54759 Nonbonded interactions: 124240 Sorted by model distance: nonbonded pdb=" O SER B 498 " pdb=" OG1 THR B 502 " model vdw 1.947 2.440 nonbonded pdb=" OG1 THR B 31 " pdb=" OE1 GLU B 32 " model vdw 1.963 2.440 nonbonded pdb=" O LEU A 693 " pdb=" O HOH A 901 " model vdw 2.003 2.440 nonbonded pdb=" O LEU B 693 " pdb=" O HOH B 901 " model vdw 2.005 2.440 nonbonded pdb=" O LEU B 124 " pdb=" O HOH B 902 " model vdw 2.008 2.440 ... (remaining 124235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.030 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 37.750 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 0.489 13462 Z= 0.633 Angle : 0.692 20.488 18206 Z= 0.387 Chirality : 0.064 1.378 1858 Planarity : 0.004 0.046 2372 Dihedral : 17.346 88.410 4916 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.23 % Allowed : 14.96 % Favored : 83.82 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.34 % 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: 0.41 (0.21), residues: 1618 helix: 0.96 (0.24), residues: 482 sheet: 0.86 (0.29), residues: 294 loop : -0.29 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.006 0.001 HIS A 245 PHE 0.014 0.002 PHE B 360 TYR 0.016 0.002 TYR A 14 ARG 0.006 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.540 Fit side-chains REVERT: A 91 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7979 (mtt180) REVERT: A 142 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7787 (tttm) REVERT: A 540 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6821 (mtm-85) REVERT: A 544 GLN cc_start: 0.7904 (mt0) cc_final: 0.7637 (mt0) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 1.6416 time to fit residues: 259.6665 Evaluate side-chains 143 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 HIS B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13462 Z= 0.415 Angle : 0.701 7.666 18206 Z= 0.393 Chirality : 0.053 0.150 1858 Planarity : 0.006 0.061 2372 Dihedral : 7.219 56.236 1819 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 12.72 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.21 (0.21), residues: 1618 helix: 0.65 (0.23), residues: 484 sheet: 0.87 (0.28), residues: 306 loop : -0.39 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 332 HIS 0.007 0.002 HIS A 245 PHE 0.019 0.003 PHE A 370 TYR 0.023 0.003 TYR A 463 ARG 0.005 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 1.577 Fit side-chains REVERT: A 258 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: A 275 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: A 315 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.7545 (mmtp) REVERT: A 536 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: A 544 GLN cc_start: 0.7928 (mt0) cc_final: 0.7699 (mt0) REVERT: B 258 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 272 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: B 275 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: B 290 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: B 561 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7741 (mm-30) outliers start: 43 outliers final: 22 residues processed: 157 average time/residue: 1.5248 time to fit residues: 259.0920 Evaluate side-chains 157 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 125 ASN B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13462 Z= 0.313 Angle : 0.633 7.300 18206 Z= 0.356 Chirality : 0.050 0.148 1858 Planarity : 0.005 0.046 2372 Dihedral : 6.525 54.974 1804 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.32 % Allowed : 12.93 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.25 (0.21), residues: 1618 helix: 0.73 (0.24), residues: 486 sheet: 0.92 (0.28), residues: 306 loop : -0.42 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 332 HIS 0.006 0.001 HIS B 245 PHE 0.019 0.002 PHE A 370 TYR 0.020 0.002 TYR B 463 ARG 0.004 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.565 Fit side-chains REVERT: A 117 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: A 258 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 275 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: A 290 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 315 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.7502 (mmtp) REVERT: A 536 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: A 544 GLN cc_start: 0.7871 (mt0) cc_final: 0.7605 (mt0) REVERT: B 91 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8024 (mtt180) REVERT: B 258 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: B 272 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: B 275 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: B 290 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: B 561 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7789 (mm-30) outliers start: 46 outliers final: 26 residues processed: 164 average time/residue: 1.5967 time to fit residues: 282.1610 Evaluate side-chains 166 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13462 Z= 0.193 Angle : 0.546 6.517 18206 Z= 0.307 Chirality : 0.046 0.145 1858 Planarity : 0.004 0.043 2372 Dihedral : 6.038 50.610 1803 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.53 % Allowed : 13.87 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.44 (0.21), residues: 1618 helix: 0.97 (0.24), residues: 486 sheet: 1.06 (0.29), residues: 296 loop : -0.35 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 332 HIS 0.005 0.001 HIS B 245 PHE 0.019 0.002 PHE A 370 TYR 0.016 0.002 TYR A 14 ARG 0.005 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.470 Fit side-chains REVERT: A 142 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7785 (tttm) REVERT: A 258 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: A 275 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: A 536 GLU cc_start: 0.7096 (mp0) cc_final: 0.6844 (mm-30) REVERT: A 538 GLU cc_start: 0.7347 (mp0) cc_final: 0.7081 (mp0) REVERT: A 544 GLN cc_start: 0.7847 (mt0) cc_final: 0.7631 (mt0) REVERT: B 258 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: B 290 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: B 538 GLU cc_start: 0.7397 (mp0) cc_final: 0.7044 (mp0) outliers start: 35 outliers final: 25 residues processed: 155 average time/residue: 1.5341 time to fit residues: 256.9731 Evaluate side-chains 155 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 0.0670 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 389 GLN A 445 ASN B 11 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 445 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13462 Z= 0.116 Angle : 0.468 5.584 18206 Z= 0.263 Chirality : 0.043 0.140 1858 Planarity : 0.004 0.040 2372 Dihedral : 5.225 45.482 1802 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.52 % Allowed : 14.74 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.70 (0.21), residues: 1618 helix: 1.29 (0.24), residues: 490 sheet: 1.10 (0.29), residues: 294 loop : -0.23 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 724 HIS 0.004 0.001 HIS B 245 PHE 0.019 0.001 PHE A 370 TYR 0.011 0.001 TYR A 14 ARG 0.010 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.523 Fit side-chains REVERT: A 142 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7697 (tttm) REVERT: A 327 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8545 (ptp90) REVERT: A 536 GLU cc_start: 0.7064 (mp0) cc_final: 0.6862 (mm-30) REVERT: A 538 GLU cc_start: 0.7367 (mp0) cc_final: 0.7127 (mp0) REVERT: A 544 GLN cc_start: 0.7856 (mt0) cc_final: 0.7649 (mt0) REVERT: B 91 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: B 159 TYR cc_start: 0.8274 (t80) cc_final: 0.8047 (t80) REVERT: B 327 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8543 (ptp90) outliers start: 21 outliers final: 8 residues processed: 147 average time/residue: 1.6331 time to fit residues: 259.0172 Evaluate side-chains 136 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 445 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 445 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13462 Z= 0.356 Angle : 0.642 7.625 18206 Z= 0.360 Chirality : 0.051 0.151 1858 Planarity : 0.005 0.052 2372 Dihedral : 5.668 45.412 1797 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.82 % Allowed : 14.16 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.39 (0.21), residues: 1618 helix: 0.91 (0.24), residues: 484 sheet: 1.11 (0.29), residues: 296 loop : -0.40 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.003 PHE B 370 TYR 0.021 0.002 TYR A 14 ARG 0.006 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.520 Fit side-chains REVERT: A 144 LYS cc_start: 0.8375 (tptp) cc_final: 0.8116 (tptp) REVERT: A 258 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 275 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 290 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: A 354 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7459 (mp) REVERT: A 536 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: A 538 GLU cc_start: 0.7389 (mp0) cc_final: 0.7094 (mp0) REVERT: B 91 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8024 (mtt180) REVERT: B 258 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: B 290 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: B 377 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7779 (mmm-85) REVERT: B 538 GLU cc_start: 0.7474 (mp0) cc_final: 0.7084 (mp0) REVERT: B 561 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7754 (mm-30) outliers start: 39 outliers final: 20 residues processed: 159 average time/residue: 1.6206 time to fit residues: 277.1422 Evaluate side-chains 157 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 579 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13462 Z= 0.148 Angle : 0.505 5.990 18206 Z= 0.284 Chirality : 0.044 0.141 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.165 45.905 1797 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 15.10 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.64 (0.21), residues: 1618 helix: 1.24 (0.24), residues: 482 sheet: 1.13 (0.29), residues: 294 loop : -0.27 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.001 PHE A 370 TYR 0.014 0.001 TYR A 14 ARG 0.006 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.606 Fit side-chains REVERT: A 142 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7781 (tttp) REVERT: A 538 GLU cc_start: 0.7384 (mp0) cc_final: 0.7119 (mp0) REVERT: B 258 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: B 538 GLU cc_start: 0.7405 (mp0) cc_final: 0.7035 (mp0) REVERT: B 561 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7722 (mm-30) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 1.6238 time to fit residues: 258.9872 Evaluate side-chains 145 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13462 Z= 0.241 Angle : 0.570 6.894 18206 Z= 0.319 Chirality : 0.047 0.147 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.348 45.710 1795 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.10 % Allowed : 15.03 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.58 (0.21), residues: 1618 helix: 1.14 (0.24), residues: 484 sheet: 1.10 (0.29), residues: 296 loop : -0.28 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE B 370 TYR 0.018 0.002 TYR A 14 ARG 0.008 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.709 Fit side-chains REVERT: A 142 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7820 (tttp) REVERT: A 258 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: A 290 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: A 354 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 538 GLU cc_start: 0.7440 (mp0) cc_final: 0.7150 (mp0) REVERT: B 258 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 354 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7322 (mp) REVERT: B 538 GLU cc_start: 0.7488 (mp0) cc_final: 0.7100 (mp0) REVERT: B 561 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7729 (mm-30) outliers start: 29 outliers final: 19 residues processed: 151 average time/residue: 1.6408 time to fit residues: 267.3479 Evaluate side-chains 155 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 0.0050 chunk 131 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13462 Z= 0.120 Angle : 0.473 5.628 18206 Z= 0.265 Chirality : 0.043 0.140 1858 Planarity : 0.004 0.042 2372 Dihedral : 4.862 45.388 1795 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.23 % Allowed : 16.04 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.73 (0.21), residues: 1618 helix: 1.35 (0.24), residues: 488 sheet: 1.13 (0.29), residues: 294 loop : -0.23 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 724 HIS 0.004 0.001 HIS B 245 PHE 0.019 0.001 PHE B 370 TYR 0.011 0.001 TYR B 308 ARG 0.007 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.649 Fit side-chains REVERT: A 142 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7777 (tttp) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 1.6534 time to fit residues: 254.7718 Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13462 Z= 0.288 Angle : 0.598 7.176 18206 Z= 0.335 Chirality : 0.048 0.145 1858 Planarity : 0.005 0.045 2372 Dihedral : 5.379 46.060 1795 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.16 % Allowed : 16.04 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.58 (0.21), residues: 1618 helix: 1.13 (0.24), residues: 484 sheet: 1.13 (0.29), residues: 296 loop : -0.28 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 332 HIS 0.004 0.001 HIS B 245 PHE 0.017 0.002 PHE B 370 TYR 0.020 0.002 TYR B 14 ARG 0.007 0.001 ARG A 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.609 Fit side-chains REVERT: A 142 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7834 (tttp) REVERT: A 258 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: A 538 GLU cc_start: 0.7481 (mp0) cc_final: 0.7179 (mp0) REVERT: B 258 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 354 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7354 (mp) REVERT: B 538 GLU cc_start: 0.7522 (mp0) cc_final: 0.7126 (mp0) REVERT: B 561 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7689 (mm-30) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 1.6388 time to fit residues: 248.6600 Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 561 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101963 restraints weight = 13430.719| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.20 r_work: 0.3168 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13462 Z= 0.244 Angle : 0.575 6.857 18206 Z= 0.322 Chirality : 0.047 0.147 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.360 45.537 1795 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.45 % Allowed : 15.68 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.56 (0.21), residues: 1618 helix: 1.09 (0.24), residues: 484 sheet: 1.11 (0.29), residues: 296 loop : -0.28 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE B 370 TYR 0.018 0.002 TYR A 14 ARG 0.008 0.000 ARG A 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.47 seconds wall clock time: 88 minutes 46.16 seconds (5326.16 seconds total)