Starting phenix.real_space_refine on Thu Apr 11 17:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sun_40768/04_2024/8sun_40768_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sun_40768/04_2024/8sun_40768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sun_40768/04_2024/8sun_40768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sun_40768/04_2024/8sun_40768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sun_40768/04_2024/8sun_40768_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sun_40768/04_2024/8sun_40768_trim_updated.pdb" } resolution = 3.12 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= 0.005 sd= 0.081 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7802 2.51 5 N 1898 2.21 5 O 2099 1.98 5 F 3 1.80 5 H 11544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23420 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11125 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12188 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 64 Unusual residues: {' CA': 2, 'JRF': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.82, per 1000 atoms: 0.46 Number of scatterers: 23420 At special positions: 0 Unit cell: (130.884, 87.256, 121.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 71 16.00 F 3 9.00 O 2099 8.00 N 1898 7.00 C 7802 6.00 H 11544 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.05 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.04 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " 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 Atom "HETATM23353 O5 NAG A 903 .*. O " rejected from bonding due to valence issues. Atom "HETATM23368 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG A 903 " - " ASN A 778 " " NAG B 901 " - " ASN B 362 " Time building additional restraints: 18.90 Conformation dependent library (CDL) restraints added in 2.4 seconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 4 sheets defined 57.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 294 through 327 removed outlier: 3.750A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 362 through 374 removed outlier: 3.933A pdb=" N CYS A 365 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU A 366 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 407 removed outlier: 3.599A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 485 Processing helix chain 'A' and resid 504 through 539 removed outlier: 4.065A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 572 removed outlier: 5.416A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 602 through 625 Processing helix chain 'A' and resid 627 through 633 Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 663 through 680 Processing helix chain 'A' and resid 688 through 709 removed outlier: 4.006A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 746 removed outlier: 3.944A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 759 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 826 through 855 Processing helix chain 'A' and resid 862 through 870 removed outlier: 3.744A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 108 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.527A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 294 through 326 removed outlier: 3.664A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 366 through 375 Processing helix chain 'B' and resid 377 through 407 removed outlier: 4.012A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 456 through 486 Processing helix chain 'B' and resid 505 through 538 removed outlier: 4.075A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 572 removed outlier: 5.208A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 602 through 639 Proline residue: B 628 - end of helix removed outlier: 4.108A pdb=" N ARG B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 655 removed outlier: 3.671A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 680 Processing helix chain 'B' and resid 688 through 709 removed outlier: 4.102A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 746 removed outlier: 3.749A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 826 through 856 Processing helix chain 'B' and resid 862 through 867 Processing sheet with id= A, first strand: chain 'A' and resid 244 through 246 removed outlier: 3.822A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 782 through 785 Processing sheet with id= C, first strand: chain 'B' and resid 244 through 246 removed outlier: 4.149A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 76 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 221 through 225 removed outlier: 3.823A pdb=" N TYR B 222 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS B 230 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL B 224 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 605 hydrogen bonds defined for protein. 1779 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: 8.80 Time building geometry restraints manager: 19.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11532 1.02 - 1.22: 26 1.22 - 1.42: 5277 1.42 - 1.62: 6801 1.62 - 1.82: 112 Bond restraints: 23748 Sorted by residual: bond pdb=" ND2 ASN A 778 " pdb="HD21 ASN A 778 " ideal model delta sigma weight residual 0.860 1.006 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C LEU B 371 " pdb=" O LEU B 371 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.19e-02 7.06e+03 4.99e+01 bond pdb=" ND2 ASN B 562 " pdb="HD22 ASN B 562 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 562 " pdb="HD21 ASN B 562 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN B 785 " pdb="HD21 ASN B 785 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.53e+01 ... (remaining 23743 not shown) Histogram of bond angle deviations from ideal: 73.15 - 94.51: 24 94.51 - 115.87: 29450 115.87 - 137.23: 13295 137.23 - 158.59: 0 158.59 - 179.95: 1 Bond angle restraints: 42770 Sorted by residual: angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 73.97 36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.15 35.85 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.66 35.34 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.71 35.29 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 109.00 73.76 35.24 3.00e+00 1.11e-01 1.38e+02 ... (remaining 42765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10214 17.66 - 35.32: 860 35.32 - 52.97: 229 52.97 - 70.63: 56 70.63 - 88.29: 21 Dihedral angle restraints: 11380 sinusoidal: 5997 harmonic: 5383 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -168.22 82.22 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CA VAL A 625 " pdb=" C VAL A 625 " pdb=" N LEU A 626 " pdb=" CA LEU A 626 " ideal model delta harmonic sigma weight residual 180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual -86.00 -39.85 -46.15 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 11377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1805 0.197 - 0.395: 7 0.395 - 0.592: 2 0.592 - 0.789: 1 0.789 - 0.986: 1 Chirality restraints: 1816 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 778 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -3.39 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -1.80 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 1813 not shown) Planarity restraints: 3425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 785 " 0.006 2.00e-02 2.50e+03 1.89e-01 4.45e+02 pdb=" CG ASN B 785 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 785 " -0.122 2.00e-02 2.50e+03 pdb=" ND2 ASN B 785 " 0.310 2.00e-02 2.50e+03 pdb="HD21 ASN B 785 " -0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 778 " 0.222 2.00e-02 2.50e+03 1.63e-01 3.98e+02 pdb=" CG ASN A 778 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 778 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 778 " -0.214 2.00e-02 2.50e+03 pdb="HD21 ASN A 778 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG A 903 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 559 " -0.036 2.00e-02 2.50e+03 3.74e-02 2.09e+01 pdb=" CD GLN B 559 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 559 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 GLN B 559 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 559 " 0.053 2.00e-02 2.50e+03 pdb="HE22 GLN B 559 " -0.056 2.00e-02 2.50e+03 ... (remaining 3422 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 66 1.82 - 2.52: 18245 2.52 - 3.21: 71182 3.21 - 3.91: 90044 3.91 - 4.60: 140014 Nonbonded interactions: 319551 Sorted by model distance: nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A 904 " model vdw 1.130 2.390 nonbonded pdb=" HZ2 LYS B 370 " pdb=" N07 JRF B 906 " model vdw 1.219 2.600 nonbonded pdb=" CD GLU A 667 " pdb="CA CA A 904 " model vdw 1.234 2.690 nonbonded pdb=" OD1 ASN B 785 " pdb=" O5 NAG B 903 " model vdw 1.281 2.800 nonbonded pdb="HH22 ARG A 808 " pdb=" O7 NAG A 903 " model vdw 1.283 1.850 ... (remaining 319546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 361 or (resid 362 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 363 through 777 or (resid 778 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or na \ me H or name HA or name HB2 or name HB3)) or resid 779 through 868 or resid 901) \ ) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 634 or resid 647 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 784 or ( \ resid 785 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 786 t \ hrough 857 or (resid 858 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 859 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or resid 860 through 868 or res \ id 903)) } 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: 0.730 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: 0.340 Extract box with map and model: 4.680 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 76.360 Find NCS groups from input model: 1.190 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 0.084 12204 Z= 0.271 Angle : 0.641 10.339 16571 Z= 0.372 Chirality : 0.056 0.986 1816 Planarity : 0.005 0.075 2057 Dihedral : 14.215 88.290 4488 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 0.40 % Allowed : 0.48 % Favored : 99.12 % Cbeta Deviations : 0.07 % 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: 0.78 (0.22), residues: 1420 helix: 1.74 (0.18), residues: 827 sheet: -0.01 (0.69), residues: 54 loop : -1.42 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 359 HIS 0.005 0.001 HIS A 108 PHE 0.013 0.001 PHE A 393 TYR 0.021 0.001 TYR B 101 ARG 0.014 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7945 (mtm) cc_final: 0.7557 (mtm) REVERT: A 525 ASN cc_start: 0.7305 (t0) cc_final: 0.6480 (t0) REVERT: A 529 GLU cc_start: 0.7678 (pt0) cc_final: 0.7439 (mt-10) REVERT: B 616 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7658 (tttp) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.4944 time to fit residues: 122.2019 Evaluate side-chains 130 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 616 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12204 Z= 0.195 Angle : 0.525 14.441 16571 Z= 0.276 Chirality : 0.045 0.485 1816 Planarity : 0.004 0.050 2057 Dihedral : 6.325 72.903 1727 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.56 % Allowed : 4.94 % Favored : 94.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1420 helix: 1.91 (0.18), residues: 827 sheet: -0.23 (0.76), residues: 45 loop : -1.34 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 359 HIS 0.002 0.001 HIS A 108 PHE 0.025 0.001 PHE A 461 TYR 0.011 0.001 TYR A 305 ARG 0.008 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7498 (pp30) cc_final: 0.7293 (pp30) REVERT: A 525 ASN cc_start: 0.7349 (t0) cc_final: 0.6859 (t0) outliers start: 7 outliers final: 7 residues processed: 142 average time/residue: 0.4744 time to fit residues: 102.9032 Evaluate side-chains 137 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12204 Z= 0.243 Angle : 0.527 14.303 16571 Z= 0.282 Chirality : 0.045 0.485 1816 Planarity : 0.004 0.051 2057 Dihedral : 5.996 69.263 1723 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.64 % Allowed : 7.73 % Favored : 91.63 % Cbeta Deviations : 0.07 % 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: 0.86 (0.22), residues: 1420 helix: 1.84 (0.18), residues: 828 sheet: -0.24 (0.70), residues: 53 loop : -1.42 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 359 HIS 0.003 0.001 HIS B 768 PHE 0.020 0.001 PHE B 253 TYR 0.012 0.001 TYR B 580 ARG 0.009 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7423 (pp30) cc_final: 0.7199 (pp30) REVERT: B 629 TRP cc_start: 0.7949 (t60) cc_final: 0.7686 (t60) outliers start: 8 outliers final: 8 residues processed: 140 average time/residue: 0.4888 time to fit residues: 103.3446 Evaluate side-chains 134 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.0970 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12204 Z= 0.136 Angle : 0.483 14.988 16571 Z= 0.252 Chirality : 0.044 0.491 1816 Planarity : 0.004 0.048 2057 Dihedral : 5.859 79.847 1723 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.40 % Allowed : 8.61 % Favored : 91.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1420 helix: 2.06 (0.18), residues: 834 sheet: -0.20 (0.70), residues: 53 loop : -1.28 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.004 0.001 HIS B 108 PHE 0.018 0.001 PHE B 253 TYR 0.010 0.001 TYR B 77 ARG 0.006 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7414 (pp30) cc_final: 0.7189 (pp30) REVERT: A 569 TYR cc_start: 0.7703 (t80) cc_final: 0.7445 (t80) REVERT: B 629 TRP cc_start: 0.7916 (t60) cc_final: 0.7654 (t60) REVERT: B 742 MET cc_start: 0.7703 (mmm) cc_final: 0.7146 (mmm) outliers start: 5 outliers final: 5 residues processed: 135 average time/residue: 0.4918 time to fit residues: 99.3139 Evaluate side-chains 136 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 653 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 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 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12204 Z= 0.229 Angle : 0.506 14.659 16571 Z= 0.268 Chirality : 0.045 0.490 1816 Planarity : 0.004 0.047 2057 Dihedral : 5.850 83.015 1723 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.80 % Allowed : 8.92 % Favored : 90.28 % Cbeta Deviations : 0.07 % 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: 1.05 (0.23), residues: 1420 helix: 1.98 (0.18), residues: 834 sheet: -0.22 (0.70), residues: 53 loop : -1.36 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.004 0.001 HIS B 108 PHE 0.015 0.001 PHE B 556 TYR 0.012 0.001 TYR B 580 ARG 0.004 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7406 (pp30) cc_final: 0.7171 (pp30) REVERT: A 569 TYR cc_start: 0.7777 (t80) cc_final: 0.7505 (t80) REVERT: B 629 TRP cc_start: 0.7993 (t60) cc_final: 0.7729 (t60) REVERT: B 742 MET cc_start: 0.7722 (mmm) cc_final: 0.7289 (mmm) outliers start: 10 outliers final: 8 residues processed: 140 average time/residue: 0.4680 time to fit residues: 99.3144 Evaluate side-chains 138 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 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 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12204 Z= 0.238 Angle : 0.514 14.847 16571 Z= 0.274 Chirality : 0.045 0.492 1816 Planarity : 0.004 0.048 2057 Dihedral : 5.777 89.992 1723 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.80 % Allowed : 9.48 % Favored : 89.72 % Cbeta Deviations : 0.07 % 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: 0.94 (0.23), residues: 1420 helix: 1.91 (0.18), residues: 836 sheet: -0.29 (0.71), residues: 53 loop : -1.45 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.005 0.001 HIS B 108 PHE 0.025 0.001 PHE A 461 TYR 0.019 0.001 TYR A 305 ARG 0.005 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7419 (pp30) cc_final: 0.7198 (pp30) REVERT: A 569 TYR cc_start: 0.7786 (t80) cc_final: 0.7554 (t80) REVERT: B 629 TRP cc_start: 0.8000 (t60) cc_final: 0.7753 (t60) REVERT: B 742 MET cc_start: 0.7646 (mmm) cc_final: 0.7201 (mmm) outliers start: 10 outliers final: 9 residues processed: 142 average time/residue: 0.4665 time to fit residues: 100.6942 Evaluate side-chains 141 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12204 Z= 0.333 Angle : 0.558 14.608 16571 Z= 0.302 Chirality : 0.046 0.491 1816 Planarity : 0.005 0.049 2057 Dihedral : 5.932 86.362 1723 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.12 % Allowed : 9.80 % Favored : 89.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1420 helix: 1.66 (0.18), residues: 837 sheet: -0.33 (0.72), residues: 53 loop : -1.59 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.005 0.001 HIS B 768 PHE 0.019 0.002 PHE B 556 TYR 0.014 0.002 TYR B 580 ARG 0.006 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7415 (pp30) cc_final: 0.7183 (pp30) REVERT: A 569 TYR cc_start: 0.7947 (t80) cc_final: 0.7739 (t80) REVERT: B 742 MET cc_start: 0.7649 (mmm) cc_final: 0.7234 (mmm) outliers start: 14 outliers final: 13 residues processed: 146 average time/residue: 0.4874 time to fit residues: 107.5415 Evaluate side-chains 145 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.0050 chunk 12 optimal weight: 40.0000 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12204 Z= 0.142 Angle : 0.490 15.585 16571 Z= 0.257 Chirality : 0.044 0.502 1816 Planarity : 0.004 0.045 2057 Dihedral : 5.648 88.952 1723 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.56 % Allowed : 10.12 % Favored : 89.32 % Cbeta Deviations : 0.07 % 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: 1.05 (0.23), residues: 1420 helix: 1.98 (0.18), residues: 837 sheet: -0.29 (0.71), residues: 53 loop : -1.37 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 PHE 0.019 0.001 PHE A 461 TYR 0.016 0.001 TYR A 305 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 TYR cc_start: 0.7837 (t80) cc_final: 0.7572 (t80) REVERT: B 742 MET cc_start: 0.7540 (mmm) cc_final: 0.7125 (mmm) outliers start: 7 outliers final: 7 residues processed: 140 average time/residue: 0.4896 time to fit residues: 103.6388 Evaluate side-chains 137 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12204 Z= 0.266 Angle : 0.521 15.038 16571 Z= 0.278 Chirality : 0.046 0.498 1816 Planarity : 0.004 0.046 2057 Dihedral : 5.745 89.946 1723 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.64 % Allowed : 10.84 % Favored : 88.53 % Cbeta Deviations : 0.07 % 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: 0.89 (0.23), residues: 1420 helix: 1.87 (0.18), residues: 837 sheet: -0.33 (0.71), residues: 53 loop : -1.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 768 PHE 0.019 0.001 PHE A 711 TYR 0.013 0.001 TYR B 580 ARG 0.004 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 TYR cc_start: 0.7913 (t80) cc_final: 0.7677 (t80) outliers start: 8 outliers final: 7 residues processed: 140 average time/residue: 0.5076 time to fit residues: 105.6340 Evaluate side-chains 143 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 142 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12204 Z= 0.138 Angle : 0.491 15.725 16571 Z= 0.256 Chirality : 0.044 0.506 1816 Planarity : 0.004 0.045 2057 Dihedral : 5.593 87.166 1723 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.72 % Allowed : 11.16 % Favored : 88.13 % Cbeta Deviations : 0.07 % 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: 1.13 (0.23), residues: 1420 helix: 2.03 (0.18), residues: 838 sheet: -0.40 (0.69), residues: 53 loop : -1.30 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.000 HIS B 108 PHE 0.020 0.001 PHE A 711 TYR 0.013 0.001 TYR A 305 ARG 0.004 0.000 ARG A 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6669 (pt) outliers start: 9 outliers final: 7 residues processed: 139 average time/residue: 0.5163 time to fit residues: 106.4256 Evaluate side-chains 140 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 653 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 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 = 0.4261 r_free = 0.4261 target = 0.184776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126144 restraints weight = 42869.734| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.57 r_work: 0.3412 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12204 Z= 0.206 Angle : 0.509 15.129 16571 Z= 0.268 Chirality : 0.045 0.498 1816 Planarity : 0.004 0.045 2057 Dihedral : 5.586 87.587 1723 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.48 % Allowed : 11.24 % Favored : 88.29 % Cbeta Deviations : 0.07 % 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: 1.08 (0.23), residues: 1420 helix: 1.99 (0.18), residues: 838 sheet: -0.40 (0.70), residues: 53 loop : -1.33 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.003 0.001 HIS B 768 PHE 0.019 0.001 PHE A 711 TYR 0.029 0.001 TYR A 569 ARG 0.004 0.000 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4915.35 seconds wall clock time: 88 minutes 46.50 seconds (5326.50 seconds total)