Starting phenix.real_space_refine on Sat Dec 9 15:09:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzc_18774/12_2023/8qzc_18774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzc_18774/12_2023/8qzc_18774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzc_18774/12_2023/8qzc_18774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzc_18774/12_2023/8qzc_18774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzc_18774/12_2023/8qzc_18774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzc_18774/12_2023/8qzc_18774.pdb" } resolution = 3.29 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 72 5.16 5 C 7472 2.51 5 N 1888 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 883": "OD1" <-> "OD2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B GLU 577": "OE1" <-> "OE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5732 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Chain: "B" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5732 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.44, per 1000 atoms: 0.56 Number of scatterers: 11468 At special positions: 0 Unit cell: (90.283, 121.915, 113.348, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 72 16.00 O 2032 8.00 N 1888 7.00 C 7472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.02 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 2.5 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 67.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 removed outlier: 4.041A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.643A pdb=" N LYS A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.648A pdb=" N SER A 225 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.672A pdb=" N PHE A 240 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.650A pdb=" N VAL A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 316 through 358 removed outlier: 7.524A pdb=" N GLU A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N LYS A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.665A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 439 removed outlier: 3.531A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 Processing helix chain 'A' and resid 489 through 527 removed outlier: 3.724A pdb=" N ALA A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 569 removed outlier: 4.070A pdb=" N GLU A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 630 through 651 removed outlier: 3.937A pdb=" N LYS A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 693 removed outlier: 3.728A pdb=" N VAL A 689 " --> pdb=" O GLN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.652A pdb=" N GLU A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.938A pdb=" N VAL A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.933A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.783A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 removed outlier: 3.906A pdb=" N ARG A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.011A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.847A pdb=" N HIS B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.543A pdb=" N SER B 225 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.726A pdb=" N PHE B 240 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 241 " --> pdb=" O ASP B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 241' Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.631A pdb=" N VAL B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 316 through 358 removed outlier: 7.512A pdb=" N GLU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N LYS B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.662A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 439 removed outlier: 3.523A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 489 through 527 removed outlier: 3.715A pdb=" N ALA B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 569 removed outlier: 4.068A pdb=" N GLU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 569 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 630 through 651 removed outlier: 3.959A pdb=" N LYS B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 693 removed outlier: 3.701A pdb=" N VAL B 689 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 716 removed outlier: 3.655A pdb=" N GLU B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.921A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.942A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.780A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 removed outlier: 3.893A pdb=" N ARG B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 3.893A pdb=" N ALA A 279 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190 removed outlier: 3.525A pdb=" N THR A 187 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.939A pdb=" N ALA B 279 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 removed outlier: 3.583A pdb=" N THR B 187 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813 661 hydrogen bonds defined for protein. 1947 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: 3.29 Time building geometry restraints manager: 5.31 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: 3562 1.34 - 1.46: 2914 1.46 - 1.58: 5160 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11754 Sorted by residual: bond pdb=" CB GLU A 555 " pdb=" CG GLU A 555 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB GLU B 555 " pdb=" CG GLU B 555 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" SD MET A 416 " pdb=" CE MET A 416 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" SD MET B 416 " pdb=" CE MET B 416 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 2.01e+00 bond pdb=" CB ASP B 883 " pdb=" CG ASP B 883 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 ... (remaining 11749 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.28: 243 105.28 - 112.48: 5685 112.48 - 119.68: 4133 119.68 - 126.88: 5693 126.88 - 134.09: 158 Bond angle restraints: 15912 Sorted by residual: angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C TYR B 288 " pdb=" N GLU B 289 " pdb=" CA GLU B 289 " ideal model delta sigma weight residual 122.08 127.90 -5.82 1.47e+00 4.63e-01 1.56e+01 angle pdb=" CB MET B 424 " pdb=" CG MET B 424 " pdb=" SD MET B 424 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C TYR A 288 " pdb=" N GLU A 289 " pdb=" CA GLU A 289 " ideal model delta sigma weight residual 122.08 127.81 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" CA LEU B 191 " pdb=" CB LEU B 191 " pdb=" CG LEU B 191 " ideal model delta sigma weight residual 116.30 129.72 -13.42 3.50e+00 8.16e-02 1.47e+01 ... (remaining 15907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 6166 16.03 - 32.06: 702 32.06 - 48.08: 127 48.08 - 64.11: 21 64.11 - 80.14: 6 Dihedral angle restraints: 7022 sinusoidal: 2870 harmonic: 4152 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -149.60 63.60 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -149.37 63.37 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -46.12 -39.88 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1314 0.051 - 0.102: 352 0.102 - 0.154: 80 0.154 - 0.205: 3 0.205 - 0.256: 5 Chirality restraints: 1754 Sorted by residual: chirality pdb=" CA GLU B 425 " pdb=" N GLU B 425 " pdb=" C GLU B 425 " pdb=" CB GLU B 425 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL A 569 " pdb=" CA VAL A 569 " pdb=" CG1 VAL A 569 " pdb=" CG2 VAL A 569 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL B 750 " pdb=" CA VAL B 750 " pdb=" CG1 VAL B 750 " pdb=" CG2 VAL B 750 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1751 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 176 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 177 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 176 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO B 177 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 406 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO B 407 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.025 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2328 2.78 - 3.31: 10850 3.31 - 3.84: 18851 3.84 - 4.37: 21116 4.37 - 4.90: 37307 Nonbonded interactions: 90452 Sorted by model distance: nonbonded pdb=" O VAL B 590 " pdb=" OG1 THR B 594 " model vdw 2.246 2.440 nonbonded pdb=" O VAL A 590 " pdb=" OG1 THR A 594 " model vdw 2.249 2.440 nonbonded pdb=" O LYS A 175 " pdb=" OG1 THR A 178 " model vdw 2.290 2.440 nonbonded pdb=" OG SER A 387 " pdb=" OD2 ASP A 828 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 387 " pdb=" OD2 ASP B 828 " model vdw 2.291 2.440 ... (remaining 90447 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: 2.240 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: 9.600 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.920 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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:3.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.004 0.047 11754 Z= 0.246 Angle : 0.813 13.424 15912 Z= 0.420 Chirality : 0.049 0.256 1754 Planarity : 0.006 0.058 1998 Dihedral : 13.360 80.141 4310 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1382 helix: -0.05 (0.16), residues: 856 sheet: -1.79 (0.99), residues: 28 loop : -2.35 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 230 PHE 0.028 0.002 PHE B 324 TYR 0.026 0.002 TYR B 222 ARG 0.007 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2513 time to fit residues: 61.2398 Evaluate side-chains 129 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11754 Z= 0.321 Angle : 0.636 8.448 15912 Z= 0.332 Chirality : 0.044 0.188 1754 Planarity : 0.004 0.045 1998 Dihedral : 4.382 17.431 1546 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.76 % Allowed : 7.53 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1382 helix: 0.77 (0.17), residues: 854 sheet: -2.89 (0.60), residues: 58 loop : -2.07 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 427 HIS 0.008 0.001 HIS B 402 PHE 0.019 0.002 PHE A 126 TYR 0.017 0.002 TYR B 838 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.338 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 159 average time/residue: 0.2344 time to fit residues: 54.1036 Evaluate side-chains 144 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1023 time to fit residues: 4.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11754 Z= 0.203 Angle : 0.563 7.769 15912 Z= 0.291 Chirality : 0.040 0.189 1754 Planarity : 0.004 0.036 1998 Dihedral : 4.141 15.593 1546 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.88 % Allowed : 10.02 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1382 helix: 1.24 (0.17), residues: 854 sheet: -3.05 (0.58), residues: 58 loop : -2.00 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 PHE 0.030 0.001 PHE A 126 TYR 0.013 0.001 TYR A 838 ARG 0.003 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.314 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 146 average time/residue: 0.2540 time to fit residues: 52.9298 Evaluate side-chains 130 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1047 time to fit residues: 2.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 229 GLN B 692 ASN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11754 Z= 0.214 Angle : 0.572 7.807 15912 Z= 0.294 Chirality : 0.040 0.181 1754 Planarity : 0.003 0.032 1998 Dihedral : 4.172 22.638 1546 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.72 % Allowed : 11.30 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1382 helix: 1.41 (0.17), residues: 854 sheet: -3.07 (0.60), residues: 58 loop : -1.95 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 PHE 0.023 0.001 PHE A 126 TYR 0.013 0.001 TYR A 838 ARG 0.002 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.310 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.2524 time to fit residues: 52.4520 Evaluate side-chains 132 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1046 time to fit residues: 2.6319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11754 Z= 0.308 Angle : 0.622 8.363 15912 Z= 0.321 Chirality : 0.042 0.183 1754 Planarity : 0.004 0.033 1998 Dihedral : 4.327 21.180 1546 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.76 % Allowed : 11.86 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1382 helix: 1.30 (0.17), residues: 854 sheet: -3.07 (0.64), residues: 58 loop : -2.02 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.006 0.001 HIS A 402 PHE 0.020 0.002 PHE B 126 TYR 0.016 0.002 TYR A 838 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.301 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 152 average time/residue: 0.2491 time to fit residues: 54.2668 Evaluate side-chains 140 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1071 time to fit residues: 4.0833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 135 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11754 Z= 0.173 Angle : 0.555 8.459 15912 Z= 0.283 Chirality : 0.040 0.201 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.080 18.032 1546 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.32 % Allowed : 13.62 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.23), residues: 1382 helix: 1.61 (0.18), residues: 854 sheet: -3.26 (0.61), residues: 60 loop : -1.91 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.020 0.001 PHE A 126 TYR 0.010 0.001 TYR A 838 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.343 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 151 average time/residue: 0.2476 time to fit residues: 53.5371 Evaluate side-chains 132 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 114 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11754 Z= 0.315 Angle : 0.629 8.866 15912 Z= 0.325 Chirality : 0.043 0.182 1754 Planarity : 0.004 0.033 1998 Dihedral : 4.293 18.716 1546 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.88 % Allowed : 14.34 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1382 helix: 1.36 (0.17), residues: 854 sheet: -3.29 (0.62), residues: 60 loop : -1.95 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 PHE 0.019 0.002 PHE A 126 TYR 0.016 0.002 TYR A 838 ARG 0.004 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.315 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 146 average time/residue: 0.2319 time to fit residues: 49.7645 Evaluate side-chains 132 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1255 time to fit residues: 2.4207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11754 Z= 0.163 Angle : 0.573 9.175 15912 Z= 0.289 Chirality : 0.040 0.235 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.116 17.802 1546 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.72 % Allowed : 14.82 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1382 helix: 1.65 (0.18), residues: 854 sheet: -3.27 (0.61), residues: 60 loop : -1.80 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 PHE 0.019 0.001 PHE B 126 TYR 0.009 0.001 TYR A 838 ARG 0.003 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.539 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 141 average time/residue: 0.2327 time to fit residues: 48.3653 Evaluate side-chains 132 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1101 time to fit residues: 2.3662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11754 Z= 0.213 Angle : 0.595 9.229 15912 Z= 0.305 Chirality : 0.041 0.205 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.167 22.133 1546 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.64 % Allowed : 15.46 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1382 helix: 1.63 (0.18), residues: 852 sheet: -3.27 (0.61), residues: 60 loop : -1.83 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 PHE 0.018 0.001 PHE A 126 TYR 0.012 0.001 TYR A 838 ARG 0.004 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.221 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 136 average time/residue: 0.2318 time to fit residues: 47.0991 Evaluate side-chains 130 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1313 time to fit residues: 2.8323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.0370 chunk 139 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11754 Z= 0.172 Angle : 0.573 9.314 15912 Z= 0.292 Chirality : 0.040 0.234 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.064 19.126 1546 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.48 % Allowed : 15.46 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1382 helix: 1.67 (0.18), residues: 860 sheet: -3.26 (0.61), residues: 60 loop : -1.89 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 402 PHE 0.019 0.001 PHE A 126 TYR 0.009 0.001 TYR A 838 ARG 0.002 0.000 ARG A 748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.313 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 134 average time/residue: 0.2310 time to fit residues: 45.3775 Evaluate side-chains 128 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1025 time to fit residues: 2.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.188387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143187 restraints weight = 14208.250| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.17 r_work: 0.3635 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11754 Z= 0.214 Angle : 0.582 9.264 15912 Z= 0.299 Chirality : 0.041 0.221 1754 Planarity : 0.003 0.031 1998 Dihedral : 4.082 17.351 1546 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.32 % Allowed : 16.11 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1382 helix: 1.61 (0.18), residues: 858 sheet: -3.26 (0.62), residues: 60 loop : -1.90 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.019 0.001 PHE A 126 TYR 0.012 0.001 TYR A 838 ARG 0.004 0.000 ARG A 748 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.24 seconds wall clock time: 46 minutes 24.82 seconds (2784.82 seconds total)