Starting phenix.real_space_refine on Sun Jul 21 03:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/07_2024/8ut6_42531.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/07_2024/8ut6_42531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/07_2024/8ut6_42531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/07_2024/8ut6_42531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/07_2024/8ut6_42531.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/07_2024/8ut6_42531.cif" } resolution = 2.8 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8094 2.51 5 N 2314 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "E" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3843 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.42, per 1000 atoms: 0.72 Number of scatterers: 13046 At special positions: 0 Unit cell: (84.1, 122.525, 145.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2584 8.00 N 2314 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 38 " " NAG A 602 " - " ASN A 63 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 246 " " NAG A 605 " - " ASN A 285 " " NAG A 606 " - " ASN A 483 " " NAG B 1 " - " ASN A 165 " " NAG C 601 " - " ASN C 38 " " NAG C 602 " - " ASN C 63 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 246 " " NAG C 605 " - " ASN C 285 " " NAG C 606 " - " ASN C 483 " " NAG D 1 " - " ASN C 165 " " NAG E 601 " - " ASN E 38 " " NAG E 602 " - " ASN E 63 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 246 " " NAG E 605 " - " ASN E 285 " " NAG E 606 " - " ASN E 483 " " NAG F 1 " - " ASN E 165 " Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 2.1 seconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 43 sheets defined 28.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.700A pdb=" N UNK G 113 " --> pdb=" O UNK G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.783A pdb=" N UNK H 84 " --> pdb=" O UNK H 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.086A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.568A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 404 through 456 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.918A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 404 through 456 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 491 through 500 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.710A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY E 78 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 366 through 385 Processing helix chain 'E' and resid 404 through 456 Processing helix chain 'E' and resid 474 through 483 Processing helix chain 'E' and resid 491 through 500 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.545A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N UNK G 52 " --> pdb=" O UNK G 32 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N UNK G 32 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.712A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.712A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.584A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.103A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.574A pdb=" N TYR A 257 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.727A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.879A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB9, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AC1, first strand: chain 'C' and resid 360 through 366 removed outlier: 4.412A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.545A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.766A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.237A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.679A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.567A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.237A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AD5, first strand: chain 'E' and resid 361 through 365 Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD9, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.029A pdb=" N ILE E 51 " --> pdb=" O GLY E 275 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.729A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 100 through 101 removed outlier: 4.959A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.830A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AE5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE6, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.265A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 303 through 305 606 hydrogen bonds defined for protein. 1629 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: 4.94 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4407 1.34 - 1.47: 3094 1.47 - 1.59: 5707 1.59 - 1.72: 1 1.72 - 1.84: 72 Bond restraints: 13281 Sorted by residual: bond pdb=" CG PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.503 1.379 0.124 3.40e-02 8.65e+02 1.32e+01 bond pdb=" CA UNK G 118 " pdb=" CB UNK G 118 " ideal model delta sigma weight residual 1.530 1.475 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CB PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.53e+00 bond pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.96e+00 bond pdb=" CA UNK H 65 " pdb=" CB UNK H 65 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.75e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 95.04 - 102.84: 31 102.84 - 110.64: 4019 110.64 - 118.43: 6345 118.43 - 126.23: 7433 126.23 - 134.02: 199 Bond angle restraints: 18027 Sorted by residual: angle pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" N PRO C 162 " pdb=" CD PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 103.20 95.04 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C UNK H 99 " pdb=" N UNK H 100 " pdb=" CA UNK H 100 " ideal model delta sigma weight residual 121.70 114.70 7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " ideal model delta sigma weight residual 112.70 102.44 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N ARG C 354 " pdb=" CA ARG C 354 " pdb=" C ARG C 354 " ideal model delta sigma weight residual 109.24 103.65 5.59 1.67e+00 3.59e-01 1.12e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7655 17.99 - 35.98: 464 35.98 - 53.96: 158 53.96 - 71.95: 44 71.95 - 89.94: 15 Dihedral angle restraints: 8336 sinusoidal: 3427 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 43.25 49.75 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA LYS C 276 " pdb=" C LYS C 276 " pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -126.91 40.91 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1554 0.053 - 0.105: 418 0.105 - 0.158: 98 0.158 - 0.210: 7 0.210 - 0.263: 5 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 483 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 161 " -0.095 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO C 162 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 99 " -0.020 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C UNK H 99 " 0.067 2.00e-02 2.50e+03 pdb=" O UNK H 99 " -0.025 2.00e-02 2.50e+03 pdb=" N UNK H 100 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK G 116 " 0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C UNK G 116 " -0.067 2.00e-02 2.50e+03 pdb=" O UNK G 116 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK G 117 " 0.022 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 222 2.65 - 3.21: 11261 3.21 - 3.77: 20438 3.77 - 4.34: 29146 4.34 - 4.90: 47705 Nonbonded interactions: 108772 Sorted by model distance: nonbonded pdb=" O ASP E 438 " pdb=" OG SER E 442 " model vdw 2.085 2.440 nonbonded pdb=" NE2 GLN C 210 " pdb=" OD2 ASP E 101 " model vdw 2.144 2.520 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.171 2.440 nonbonded pdb=" NZ LYS A 380 " pdb=" OE1 GLU A 432 " model vdw 2.179 2.520 nonbonded pdb=" OD1 ASN C 121 " pdb=" NZ LYS C 259 " model vdw 2.208 2.520 ... (remaining 108767 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 8 through 501 or resid 601 through 606)) selection = (chain 'C' and (resid 8 through 501 or resid 601 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 9.610 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.660 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.006 0.128 13281 Z= 0.373 Angle : 0.947 12.926 18027 Z= 0.493 Chirality : 0.052 0.263 2082 Planarity : 0.006 0.132 2357 Dihedral : 13.948 89.941 5106 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.42 (0.19), residues: 1448 helix: 1.40 (0.23), residues: 351 sheet: 0.56 (0.28), residues: 294 loop : -0.29 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 421 HIS 0.009 0.001 HIS A 156 PHE 0.030 0.002 PHE A 353 TYR 0.020 0.002 TYR E 195 ARG 0.010 0.001 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7393 (t) cc_final: 0.6975 (p) REVERT: A 415 ASP cc_start: 0.7405 (t0) cc_final: 0.6859 (m-30) REVERT: C 382 ASN cc_start: 0.7884 (t0) cc_final: 0.7603 (t0) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 1.1402 time to fit residues: 167.2945 Evaluate side-chains 121 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 96 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 57 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 355 HIS A 454 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS E 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13281 Z= 0.166 Angle : 0.524 8.192 18027 Z= 0.277 Chirality : 0.042 0.239 2082 Planarity : 0.004 0.059 2357 Dihedral : 5.130 49.229 2314 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.72 % Allowed : 12.76 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.66 (0.20), residues: 1448 helix: 2.17 (0.25), residues: 354 sheet: 0.29 (0.28), residues: 285 loop : -0.25 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.004 0.001 HIS E 471 PHE 0.018 0.001 PHE A 353 TYR 0.011 0.001 TYR C 486 ARG 0.006 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.7443 (t) cc_final: 0.7008 (p) REVERT: A 75 GLN cc_start: 0.7210 (mp10) cc_final: 0.6899 (mp10) REVERT: A 82 LYS cc_start: 0.7065 (mttt) cc_final: 0.6778 (ttmm) REVERT: A 344 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5621 (mp0) REVERT: C 382 ASN cc_start: 0.7797 (t0) cc_final: 0.7538 (t0) REVERT: E 139 CYS cc_start: 0.6786 (m) cc_final: 0.6446 (m) REVERT: E 235 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7937 (m) REVERT: E 261 ARG cc_start: 0.6858 (mmt90) cc_final: 0.5937 (ptt180) outliers start: 22 outliers final: 8 residues processed: 154 average time/residue: 1.1911 time to fit residues: 201.6022 Evaluate side-chains 134 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 125 optimal weight: 0.0670 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 435 HIS E 363 GLN E 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13281 Z= 0.237 Angle : 0.552 12.872 18027 Z= 0.285 Chirality : 0.043 0.233 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.013 51.186 2312 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.43 % Allowed : 12.37 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.42 (0.20), residues: 1448 helix: 2.13 (0.26), residues: 353 sheet: -0.17 (0.28), residues: 275 loop : -0.35 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.006 0.001 HIS A 184 PHE 0.015 0.002 PHE A 353 TYR 0.011 0.002 TYR C 486 ARG 0.004 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.7482 (t) cc_final: 0.7054 (p) REVERT: A 75 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6533 (mt0) REVERT: A 340 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6126 (tt0) REVERT: A 344 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5591 (mp0) REVERT: C 382 ASN cc_start: 0.7909 (t0) cc_final: 0.7578 (t0) REVERT: E 139 CYS cc_start: 0.7110 (m) cc_final: 0.6794 (m) REVERT: E 242 ILE cc_start: 0.8050 (mt) cc_final: 0.7783 (mp) REVERT: E 261 ARG cc_start: 0.6962 (mmt90) cc_final: 0.6062 (ptt180) outliers start: 31 outliers final: 12 residues processed: 163 average time/residue: 1.1823 time to fit residues: 211.6056 Evaluate side-chains 146 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 151 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 57 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 454 GLN A 488 HIS C 363 GLN C 435 HIS E 211 GLN E 312 ASN E 363 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13281 Z= 0.389 Angle : 0.661 13.594 18027 Z= 0.339 Chirality : 0.046 0.246 2082 Planarity : 0.005 0.048 2357 Dihedral : 5.899 54.599 2312 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.21 % Allowed : 12.14 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.15 (0.20), residues: 1448 helix: 1.58 (0.26), residues: 354 sheet: -0.69 (0.27), residues: 281 loop : -0.61 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.002 HIS A 18 PHE 0.016 0.002 PHE C 87 TYR 0.014 0.002 TYR C 161 ARG 0.006 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6512 (mt0) REVERT: A 82 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6903 (ttmm) REVERT: A 189 LYS cc_start: 0.7379 (mttt) cc_final: 0.6793 (mtpm) REVERT: A 340 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6128 (tt0) REVERT: A 344 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5486 (mp0) REVERT: A 396 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: C 33 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: C 382 ASN cc_start: 0.8009 (t0) cc_final: 0.7718 (t0) REVERT: E 139 CYS cc_start: 0.7259 (m) cc_final: 0.7002 (m) REVERT: E 242 ILE cc_start: 0.8134 (mt) cc_final: 0.7878 (mp) REVERT: E 261 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6119 (ptt180) outliers start: 41 outliers final: 16 residues processed: 160 average time/residue: 1.1385 time to fit residues: 200.6198 Evaluate side-chains 140 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 211 GLN A 454 GLN C 18 HIS C 363 GLN C 435 HIS E 296 ASN E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13281 Z= 0.191 Angle : 0.515 12.101 18027 Z= 0.267 Chirality : 0.041 0.234 2082 Planarity : 0.004 0.043 2357 Dihedral : 5.158 49.991 2312 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.82 % Allowed : 13.70 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1448 helix: 1.95 (0.26), residues: 354 sheet: -0.72 (0.27), residues: 281 loop : -0.56 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.006 0.001 HIS C 18 PHE 0.012 0.001 PHE A 353 TYR 0.010 0.001 TYR E 491 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7432 (t) cc_final: 0.7025 (p) REVERT: A 75 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6514 (mt0) REVERT: A 82 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6868 (ttmm) REVERT: A 189 LYS cc_start: 0.7349 (mttt) cc_final: 0.6760 (mtpm) REVERT: A 261 ARG cc_start: 0.6879 (mtm110) cc_final: 0.6363 (mtt90) REVERT: A 340 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6064 (tt0) REVERT: A 344 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5530 (mp0) REVERT: C 382 ASN cc_start: 0.7976 (t0) cc_final: 0.7664 (t0) REVERT: E 139 CYS cc_start: 0.7076 (m) cc_final: 0.6796 (m) REVERT: E 242 ILE cc_start: 0.8127 (mt) cc_final: 0.7835 (mp) REVERT: E 261 ARG cc_start: 0.7015 (mmt90) cc_final: 0.6068 (ptt180) outliers start: 36 outliers final: 17 residues processed: 168 average time/residue: 1.1873 time to fit residues: 219.0715 Evaluate side-chains 147 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 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 57 GLN A 211 GLN A 363 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN E 296 ASN E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13281 Z= 0.294 Angle : 0.566 12.482 18027 Z= 0.290 Chirality : 0.043 0.238 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.300 53.626 2312 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.90 % Allowed : 13.55 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.08 (0.21), residues: 1448 helix: 1.91 (0.26), residues: 353 sheet: -0.84 (0.27), residues: 281 loop : -0.63 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.017 0.002 HIS C 18 PHE 0.017 0.002 PHE E 125 TYR 0.010 0.002 TYR C 486 ARG 0.004 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7491 (t) cc_final: 0.7056 (p) REVERT: A 75 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6531 (mt0) REVERT: A 82 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6902 (ttmm) REVERT: A 189 LYS cc_start: 0.7358 (mttt) cc_final: 0.6775 (mtpm) REVERT: A 340 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6157 (tt0) REVERT: A 344 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5605 (mp0) REVERT: A 402 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7964 (t) REVERT: C 382 ASN cc_start: 0.7956 (t0) cc_final: 0.7676 (t0) REVERT: E 139 CYS cc_start: 0.7162 (m) cc_final: 0.6910 (m) REVERT: E 242 ILE cc_start: 0.8165 (mt) cc_final: 0.7885 (mp) REVERT: E 261 ARG cc_start: 0.7059 (mmt90) cc_final: 0.6098 (ptt180) outliers start: 37 outliers final: 19 residues processed: 148 average time/residue: 1.2597 time to fit residues: 203.7646 Evaluate side-chains 139 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 57 GLN A 454 GLN C 18 HIS C 435 HIS E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13281 Z= 0.359 Angle : 0.617 13.259 18027 Z= 0.315 Chirality : 0.045 0.244 2082 Planarity : 0.004 0.049 2357 Dihedral : 5.693 59.893 2312 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.82 % Allowed : 13.94 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.34 (0.20), residues: 1448 helix: 1.77 (0.26), residues: 351 sheet: -0.96 (0.27), residues: 275 loop : -0.83 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.009 0.002 HIS A 18 PHE 0.018 0.002 PHE E 125 TYR 0.012 0.002 TYR C 161 ARG 0.007 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6572 (mt0) REVERT: A 82 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6885 (ttmm) REVERT: A 172 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: A 189 LYS cc_start: 0.7363 (mttt) cc_final: 0.6788 (mtpm) REVERT: A 344 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5612 (mp0) REVERT: C 33 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: C 382 ASN cc_start: 0.8013 (t0) cc_final: 0.7729 (t0) REVERT: E 242 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7908 (mp) REVERT: E 261 ARG cc_start: 0.7082 (mmt90) cc_final: 0.6120 (ptt180) REVERT: E 401 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6781 (pm20) outliers start: 36 outliers final: 19 residues processed: 148 average time/residue: 1.1584 time to fit residues: 188.4046 Evaluate side-chains 138 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 454 GLN C 18 HIS C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13281 Z= 0.217 Angle : 0.540 11.963 18027 Z= 0.277 Chirality : 0.042 0.235 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.316 55.378 2312 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.66 % Allowed : 14.88 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.12 (0.21), residues: 1448 helix: 1.95 (0.26), residues: 353 sheet: -0.84 (0.28), residues: 274 loop : -0.70 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.015 0.002 HIS C 18 PHE 0.011 0.001 PHE E 125 TYR 0.010 0.002 TYR C 94 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7457 (t) cc_final: 0.7057 (p) REVERT: A 75 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6533 (mt0) REVERT: A 82 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6829 (ttmm) REVERT: A 189 LYS cc_start: 0.7348 (mttt) cc_final: 0.6766 (mtpm) REVERT: A 344 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: C 382 ASN cc_start: 0.7989 (t0) cc_final: 0.7686 (t0) REVERT: E 242 ILE cc_start: 0.8187 (mt) cc_final: 0.7883 (mp) REVERT: E 261 ARG cc_start: 0.7062 (mmt90) cc_final: 0.6084 (ptt180) REVERT: E 401 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6792 (pm20) outliers start: 34 outliers final: 18 residues processed: 145 average time/residue: 1.1772 time to fit residues: 187.8782 Evaluate side-chains 138 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 6.9990 chunk 139 optimal weight: 0.1980 chunk 149 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN C 18 HIS C 363 GLN C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13281 Z= 0.260 Angle : 0.564 12.188 18027 Z= 0.286 Chirality : 0.043 0.298 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.404 54.863 2312 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 15.82 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1448 helix: 1.94 (0.26), residues: 353 sheet: -0.81 (0.27), residues: 281 loop : -0.72 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 127 HIS 0.005 0.001 HIS A 18 PHE 0.016 0.001 PHE E 125 TYR 0.009 0.002 TYR A 233 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7464 (t) cc_final: 0.7062 (p) REVERT: A 75 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6502 (mt0) REVERT: A 82 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6842 (ttmm) REVERT: A 189 LYS cc_start: 0.7344 (mttt) cc_final: 0.6761 (mtpm) REVERT: A 344 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5611 (mp0) REVERT: C 382 ASN cc_start: 0.7995 (t0) cc_final: 0.7680 (t0) REVERT: E 139 CYS cc_start: 0.7035 (m) cc_final: 0.6645 (m) REVERT: E 242 ILE cc_start: 0.8229 (mt) cc_final: 0.7914 (mp) outliers start: 26 outliers final: 18 residues processed: 138 average time/residue: 1.2519 time to fit residues: 189.5695 Evaluate side-chains 132 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 454 GLN C 18 HIS ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13281 Z= 0.381 Angle : 0.651 13.378 18027 Z= 0.328 Chirality : 0.046 0.366 2082 Planarity : 0.005 0.049 2357 Dihedral : 5.944 59.777 2312 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.11 % Allowed : 15.97 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1448 helix: 1.69 (0.26), residues: 353 sheet: -1.03 (0.27), residues: 273 loop : -0.83 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.007 0.002 HIS A 184 PHE 0.017 0.002 PHE E 125 TYR 0.013 0.002 TYR C 257 ARG 0.005 0.001 ARG C 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7577 (t) cc_final: 0.7116 (p) REVERT: A 75 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6531 (mt0) REVERT: A 82 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6886 (ttmm) REVERT: A 189 LYS cc_start: 0.7322 (mttt) cc_final: 0.6738 (mtpm) REVERT: A 344 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5551 (mp0) REVERT: C 382 ASN cc_start: 0.8023 (t0) cc_final: 0.7731 (t0) REVERT: E 139 CYS cc_start: 0.7147 (m) cc_final: 0.6791 (m) REVERT: E 242 ILE cc_start: 0.8175 (mt) cc_final: 0.7910 (mp) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 1.2878 time to fit residues: 193.1189 Evaluate side-chains 128 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 57 GLN A 371 GLN A 454 GLN C 18 HIS ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS E 17 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.163641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144594 restraints weight = 15305.403| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.63 r_work: 0.3537 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13281 Z= 0.218 Angle : 0.564 11.707 18027 Z= 0.288 Chirality : 0.046 0.807 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.687 54.100 2312 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.80 % Allowed : 16.60 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.22 (0.21), residues: 1448 helix: 1.86 (0.26), residues: 356 sheet: -0.97 (0.27), residues: 280 loop : -0.74 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.007 0.001 HIS A 18 PHE 0.013 0.001 PHE A 338 TYR 0.010 0.001 TYR A 233 ARG 0.004 0.000 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4250.93 seconds wall clock time: 76 minutes 6.15 seconds (4566.15 seconds total)