Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 15:57:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tai_41136/10_2023/8tai_41136_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tai_41136/10_2023/8tai_41136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tai_41136/10_2023/8tai_41136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tai_41136/10_2023/8tai_41136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tai_41136/10_2023/8tai_41136_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tai_41136/10_2023/8tai_41136_trim.pdb" } resolution = 3.1 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= 0.791 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7824 2.51 5 N 1906 2.21 5 O 2105 1.98 5 H 11607 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 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 653": "OD1" <-> "OD2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 847": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 23516 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11239 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 32, 'TRANS': 672} 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: 12190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12190 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 chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.76, per 1000 atoms: 0.42 Number of scatterers: 23516 At special positions: 0 Unit cell: (135.079, 88.095, 119.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 O 2105 8.00 N 1906 7.00 C 7824 6.00 H 11607 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=2.04 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 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 "HETATM23484 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM23455 O5 NAG A 902 .*. 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 902 " - " ASN A 785 " Time building additional restraints: 18.77 Conformation dependent library (CDL) restraints added in 1.6 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 63.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.700A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 5.732A pdb=" N ASN A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.972A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.914A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.670A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.875A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 5.427A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 removed outlier: 5.399A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.526A pdb=" N GLN A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.103A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.137A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.340A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 Processing helix chain 'A' and resid 861 through 870 removed outlier: 4.247A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 108 removed outlier: 3.626A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.641A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.534A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.679A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.928A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.745A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 488 removed outlier: 3.643A pdb=" N THR B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.944A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.229A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.906A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.361A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.992A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.571A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.682A pdb=" N TRP A 359 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.578A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 4.207A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 225 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 785 removed outlier: 3.535A pdb=" N TYR B 809 " --> pdb=" O SER B 782 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2031 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: 8.24 Time building geometry restraints manager: 19.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11595 1.03 - 1.23: 266 1.23 - 1.43: 5068 1.43 - 1.63: 6802 1.63 - 1.83: 112 Bond restraints: 23843 Sorted by residual: bond pdb=" N PHE B 52 " pdb=" H1 PHE B 52 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CG1 ILE B 472 " pdb=" CD1 ILE B 472 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CG MET A 309 " pdb=" SD MET A 309 " ideal model delta sigma weight residual 1.803 1.764 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 23838 not shown) Histogram of bond angle deviations from ideal: 73.21 - 85.37: 24 85.37 - 97.54: 0 97.54 - 109.71: 16639 109.71 - 121.88: 22519 121.88 - 134.04: 3766 Bond angle restraints: 42948 Sorted by residual: angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.18 35.82 3.00e+00 1.11e-01 1.43e+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 73.21 35.79 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ARG A 235 " pdb=" CA ARG A 235 " pdb=" HA ARG A 235 " ideal model delta sigma weight residual 109.00 73.68 35.32 3.00e+00 1.11e-01 1.39e+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 73.72 35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 74.87 35.13 3.00e+00 1.11e-01 1.37e+02 ... (remaining 42943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8811 17.99 - 35.98: 767 35.98 - 53.97: 108 53.97 - 71.96: 24 71.96 - 89.95: 10 Dihedral angle restraints: 9720 sinusoidal: 4316 harmonic: 5404 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 -175.95 89.95 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -146.29 60.29 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual -86.00 -138.27 52.27 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 9717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1812 0.309 - 0.618: 8 0.618 - 0.927: 0 0.927 - 1.236: 0 1.236 - 1.545: 1 Chirality restraints: 1821 Sorted by residual: 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 -0.99 -1.55 2.00e-01 2.50e+01 5.97e+01 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 785 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.99 0.59 2.00e-01 2.50e+01 8.83e+00 chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 1818 not shown) Planarity restraints: 3437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 785 " -0.230 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" CG ASN A 785 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 785 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 785 " 0.352 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 349 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 350 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 796 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 797 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 797 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 797 " 0.033 5.00e-02 4.00e+02 ... (remaining 3434 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1548 2.20 - 2.80: 46822 2.80 - 3.40: 64549 3.40 - 4.00: 80569 4.00 - 4.60: 125381 Nonbonded interactions: 318869 Sorted by model distance: nonbonded pdb=" O SER A 278 " pdb="HH21 ARG A 701 " model vdw 1.598 1.850 nonbonded pdb=" HA ARG B 235 " pdb=" HB3 ARG B 235 " model vdw 1.602 1.952 nonbonded pdb=" HA PHE B 215 " pdb=" HB3 PHE B 215 " model vdw 1.608 1.952 nonbonded pdb=" ND2 ASN B 362 " pdb=" O5 NAG B 901 " model vdw 1.625 2.350 nonbonded pdb=" HA ASP A 286 " pdb=" HB2 ASP A 286 " model vdw 1.630 1.952 ... (remaining 318864 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 868 or resid 901 through 902 or resid 904)) 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 638 or resid 645 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 777 or ( \ resid 778 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 779 t \ hrough 784 or (resid 785 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) \ or resid 786 through 857 or (resid 858 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 859 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or resid 860 thr \ ough 868 or resid 902 through 903 or resid 905)) } 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: 0.810 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: 0.310 Extract box with map and model: 4.910 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 70.890 Find NCS groups from input model: 1.000 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.070 12236 Z= 0.205 Angle : 0.558 12.187 16607 Z= 0.309 Chirality : 0.059 1.545 1821 Planarity : 0.004 0.060 2064 Dihedral : 13.644 89.498 4377 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: 1.32 (0.22), residues: 1426 helix: 2.26 (0.17), residues: 822 sheet: -0.83 (0.78), residues: 58 loop : -1.16 (0.26), residues: 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 184 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.947 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4723 time to fit residues: 129.8069 Evaluate side-chains 160 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12236 Z= 0.244 Angle : 0.547 7.500 16607 Z= 0.296 Chirality : 0.046 0.416 1821 Planarity : 0.004 0.050 2064 Dihedral : 3.873 22.384 1596 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 1.35 % Allowed : 5.00 % Favored : 93.65 % 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: 1.19 (0.22), residues: 1426 helix: 2.13 (0.17), residues: 830 sheet: -0.76 (0.70), residues: 65 loop : -1.25 (0.26), residues: 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 182 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.745 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 outliers start: 17 outliers final: 12 residues processed: 171 average time/residue: 0.4844 time to fit residues: 124.7312 Evaluate side-chains 165 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3012 time to fit residues: 8.9144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12236 Z= 0.205 Angle : 0.512 7.549 16607 Z= 0.278 Chirality : 0.045 0.415 1821 Planarity : 0.004 0.050 2064 Dihedral : 3.805 22.679 1596 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.71 % Allowed : 6.19 % Favored : 93.10 % 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: 1.27 (0.22), residues: 1426 helix: 2.25 (0.17), residues: 830 sheet: -1.21 (0.64), residues: 75 loop : -1.24 (0.26), residues: 521 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 173 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.972 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 170 average time/residue: 0.4848 time to fit residues: 121.7102 Evaluate side-chains 162 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.958 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2481 time to fit residues: 3.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12236 Z= 0.154 Angle : 0.488 7.647 16607 Z= 0.262 Chirality : 0.044 0.415 1821 Planarity : 0.004 0.050 2064 Dihedral : 3.701 22.458 1596 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.48 % Allowed : 7.94 % Favored : 91.59 % 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: 1.43 (0.22), residues: 1426 helix: 2.44 (0.17), residues: 826 sheet: -1.23 (0.62), residues: 75 loop : -1.24 (0.26), residues: 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 170 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 1.791 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 165 average time/residue: 0.5301 time to fit residues: 128.7673 Evaluate side-chains 156 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.877 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2970 time to fit residues: 5.1851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.6980 chunk 79 optimal weight: 0.0010 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12236 Z= 0.215 Angle : 0.502 7.563 16607 Z= 0.272 Chirality : 0.045 0.419 1821 Planarity : 0.004 0.045 2064 Dihedral : 3.722 23.014 1596 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.40 % Allowed : 8.17 % Favored : 91.43 % 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: 1.35 (0.22), residues: 1426 helix: 2.40 (0.17), residues: 826 sheet: -1.30 (0.61), residues: 75 loop : -1.30 (0.26), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 1.852 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: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 159 average time/residue: 0.4811 time to fit residues: 113.4081 Evaluate side-chains 160 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2562 time to fit residues: 4.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12236 Z= 0.179 Angle : 0.496 7.667 16607 Z= 0.267 Chirality : 0.044 0.417 1821 Planarity : 0.004 0.045 2064 Dihedral : 3.705 22.738 1596 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.40 % Allowed : 8.97 % Favored : 90.63 % 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: 1.45 (0.22), residues: 1426 helix: 2.48 (0.17), residues: 826 sheet: -1.29 (0.61), residues: 75 loop : -1.28 (0.26), residues: 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 164 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 1.903 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: symmetry clash outliers start: 5 outliers final: 2 residues processed: 161 average time/residue: 0.5091 time to fit residues: 122.2766 Evaluate side-chains 156 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2603 time to fit residues: 3.4012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12236 Z= 0.346 Angle : 0.550 7.400 16607 Z= 0.301 Chirality : 0.047 0.421 1821 Planarity : 0.004 0.046 2064 Dihedral : 3.905 23.032 1596 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.63 % Allowed : 9.05 % Favored : 90.32 % 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: 1.14 (0.22), residues: 1426 helix: 2.20 (0.17), residues: 826 sheet: -1.17 (0.66), residues: 65 loop : -1.40 (0.25), residues: 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 161 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.923 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 157 average time/residue: 0.4931 time to fit residues: 114.6983 Evaluate side-chains 155 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2979 time to fit residues: 5.5413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12236 Z= 0.238 Angle : 0.523 7.487 16607 Z= 0.283 Chirality : 0.045 0.416 1821 Planarity : 0.004 0.046 2064 Dihedral : 3.875 24.256 1596 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 0.16 % Allowed : 9.60 % Favored : 90.24 % 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: 1.20 (0.22), residues: 1426 helix: 2.25 (0.17), residues: 827 sheet: -1.19 (0.66), residues: 65 loop : -1.35 (0.26), residues: 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 162 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.888 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 160 average time/residue: 0.4992 time to fit residues: 118.7043 Evaluate side-chains 157 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2592 time to fit residues: 2.8484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12236 Z= 0.250 Angle : 0.522 7.424 16607 Z= 0.283 Chirality : 0.045 0.417 1821 Planarity : 0.004 0.047 2064 Dihedral : 3.880 23.942 1596 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % 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: 1.19 (0.22), residues: 1426 helix: 2.25 (0.17), residues: 827 sheet: -1.40 (0.62), residues: 74 loop : -1.35 (0.26), residues: 525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 155 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.711 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.4887 time to fit residues: 112.7486 Evaluate side-chains 154 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.0010 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12236 Z= 0.151 Angle : 0.494 7.583 16607 Z= 0.265 Chirality : 0.044 0.411 1821 Planarity : 0.004 0.046 2064 Dihedral : 3.760 23.743 1596 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % 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: 1.44 (0.22), residues: 1426 helix: 2.47 (0.17), residues: 827 sheet: -1.29 (0.62), residues: 74 loop : -1.27 (0.26), residues: 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 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 155 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.706 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.4643 time to fit residues: 108.0061 Evaluate side-chains 153 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.179674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122187 restraints weight = 40723.486| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.43 r_work: 0.2988 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12236 Z= 0.271 Angle : 0.525 7.419 16607 Z= 0.285 Chirality : 0.046 0.421 1821 Planarity : 0.004 0.047 2064 Dihedral : 3.845 24.262 1596 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.32 % Allowed : 10.32 % Favored : 89.37 % 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: 1.26 (0.22), residues: 1426 helix: 2.31 (0.17), residues: 827 sheet: -1.35 (0.62), residues: 74 loop : -1.32 (0.26), residues: 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4967.84 seconds wall clock time: 88 minutes 39.52 seconds (5319.52 seconds total)