Starting phenix.real_space_refine on Mon Aug 5 10:32:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/08_2024/8ut6_42531.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/08_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_42531/08_2024/8ut6_42531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/08_2024/8ut6_42531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/08_2024/8ut6_42531.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/08_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.65, per 1000 atoms: 0.66 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: 5.54 Conformation dependent library (CDL) restraints added in 2.0 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: 1.83 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: 4.55 Time building geometry restraints manager: 6.06 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 3.040 nonbonded pdb=" NE2 GLN C 210 " pdb=" OD2 ASP E 101 " model vdw 2.144 3.120 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.171 3.040 nonbonded pdb=" NZ LYS A 380 " pdb=" OE1 GLU A 432 " model vdw 2.179 3.120 nonbonded pdb=" OD1 ASN C 121 " pdb=" NZ LYS C 259 " model vdw 2.208 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 7.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.130 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.090 ------------------------------------------------------------------------------- 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 : 1.323 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: 1.2151 time to fit residues: 177.5514 Evaluate side-chains 121 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 0.0020 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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 A 211 GLN A 355 HIS A 454 GLN C 363 GLN C 435 HIS E 363 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13281 Z= 0.221 Angle : 0.575 9.071 18027 Z= 0.303 Chirality : 0.043 0.231 2082 Planarity : 0.004 0.060 2357 Dihedral : 5.490 59.924 2314 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.88 % Allowed : 12.14 % Favored : 85.98 % 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: 0.55 (0.20), residues: 1448 helix: 2.02 (0.24), residues: 353 sheet: 0.28 (0.29), residues: 273 loop : -0.31 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 421 HIS 0.004 0.001 HIS E 184 PHE 0.018 0.001 PHE A 353 TYR 0.012 0.002 TYR C 486 ARG 0.006 0.001 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 164 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.7428 (t) cc_final: 0.7017 (p) REVERT: A 82 LYS cc_start: 0.7152 (mttt) cc_final: 0.6859 (ttmm) REVERT: A 340 GLU cc_start: 0.6306 (mt-10) cc_final: 0.6016 (tt0) REVERT: A 344 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5655 (mp0) REVERT: C 382 ASN cc_start: 0.7891 (t0) cc_final: 0.7603 (t0) REVERT: E 139 CYS cc_start: 0.6960 (m) cc_final: 0.6638 (m) REVERT: E 235 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7962 (m) REVERT: E 242 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7729 (mp) REVERT: E 261 ARG cc_start: 0.6905 (mmt90) cc_final: 0.6006 (ptt180) outliers start: 24 outliers final: 6 residues processed: 154 average time/residue: 1.2344 time to fit residues: 208.6732 Evaluate side-chains 132 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS 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 E residue 235 THR Chi-restraints excluded: chain E residue 242 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 56 HIS C 363 GLN C 435 HIS E 96 ASN E 312 ASN E 363 GLN E 407 GLN E 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1589 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= 0.241 Angle : 0.561 13.195 18027 Z= 0.292 Chirality : 0.043 0.224 2082 Planarity : 0.004 0.047 2357 Dihedral : 5.111 45.382 2312 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.27 % Allowed : 12.69 % Favored : 85.04 % 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: 0.31 (0.20), residues: 1448 helix: 2.01 (0.26), residues: 353 sheet: -0.19 (0.28), residues: 273 loop : -0.42 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 421 HIS 0.005 0.001 HIS A 184 PHE 0.014 0.002 PHE E 125 TYR 0.010 0.002 TYR C 486 ARG 0.007 0.001 ARG C 321 *********************** 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 175 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.7439 (t) cc_final: 0.7049 (p) REVERT: A 340 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6112 (tt0) REVERT: A 344 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: A 396 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: C 33 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: C 344 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6379 (mp0) REVERT: C 382 ASN cc_start: 0.7924 (t0) cc_final: 0.7589 (t0) REVERT: E 139 CYS cc_start: 0.7124 (m) cc_final: 0.6822 (m) REVERT: E 235 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8045 (m) REVERT: E 242 ILE cc_start: 0.8040 (mt) cc_final: 0.7776 (mp) REVERT: E 261 ARG cc_start: 0.6995 (mmt90) cc_final: 0.6108 (ptt180) outliers start: 29 outliers final: 10 residues processed: 160 average time/residue: 1.2216 time to fit residues: 213.6912 Evaluate side-chains 136 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 225 ASN 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 E residue 187 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 462 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 0.0030 chunk 151 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 75 GLN A 454 GLN A 488 HIS C 341 ASN C 363 GLN C 435 HIS E 211 GLN E 296 ASN E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13281 Z= 0.396 Angle : 0.667 13.806 18027 Z= 0.342 Chirality : 0.046 0.250 2082 Planarity : 0.005 0.051 2357 Dihedral : 5.776 52.871 2312 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.90 % Allowed : 12.29 % Favored : 84.81 % 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: -0.23 (0.20), residues: 1448 helix: 1.53 (0.26), residues: 355 sheet: -0.71 (0.27), residues: 281 loop : -0.69 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 169 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7015 (ttmm) REVERT: A 340 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6169 (tt0) REVERT: A 344 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: A 396 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: C 382 ASN cc_start: 0.7975 (t0) cc_final: 0.7690 (t0) REVERT: E 139 CYS cc_start: 0.7241 (m) cc_final: 0.6965 (m) REVERT: E 242 ILE cc_start: 0.8185 (mt) cc_final: 0.7924 (mp) REVERT: E 261 ARG cc_start: 0.7098 (mmt90) cc_final: 0.6139 (ptt180) outliers start: 37 outliers final: 16 residues processed: 158 average time/residue: 1.2164 time to fit residues: 210.5203 Evaluate side-chains 132 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 82 LYS 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 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 312 ASN 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 267 ILE 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: 5.9990 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 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 75 GLN A 363 GLN A 371 GLN A 454 GLN C 18 HIS C 341 ASN E 296 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13281 Z= 0.284 Angle : 0.577 13.171 18027 Z= 0.298 Chirality : 0.043 0.237 2082 Planarity : 0.004 0.049 2357 Dihedral : 5.433 47.993 2312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.66 % Allowed : 13.55 % Favored : 83.79 % 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: -0.22 (0.20), residues: 1448 helix: 1.70 (0.26), residues: 355 sheet: -0.74 (0.27), residues: 273 loop : -0.75 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 421 HIS 0.006 0.001 HIS C 18 PHE 0.013 0.002 PHE A 338 TYR 0.011 0.002 TYR A 233 ARG 0.004 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 157 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7445 (t) cc_final: 0.7048 (p) REVERT: A 82 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7007 (ttmm) REVERT: A 340 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6155 (tt0) REVERT: A 344 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.5748 (mp0) REVERT: A 396 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: C 382 ASN cc_start: 0.7939 (t0) cc_final: 0.7660 (t0) REVERT: E 139 CYS cc_start: 0.7240 (m) cc_final: 0.6950 (m) REVERT: E 242 ILE cc_start: 0.8148 (mt) cc_final: 0.7870 (mp) REVERT: E 261 ARG cc_start: 0.7046 (mmt90) cc_final: 0.6098 (ptt180) outliers start: 34 outliers final: 13 residues processed: 144 average time/residue: 1.2337 time to fit residues: 194.6359 Evaluate side-chains 128 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS 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 18 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.0030 chunk 144 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN C 363 GLN E 296 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13281 Z= 0.195 Angle : 0.530 12.029 18027 Z= 0.274 Chirality : 0.042 0.232 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.110 44.627 2312 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 14.17 % Favored : 83.63 % 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: -0.07 (0.20), residues: 1448 helix: 1.99 (0.26), residues: 351 sheet: -0.70 (0.28), residues: 274 loop : -0.71 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.014 0.001 HIS C 18 PHE 0.011 0.001 PHE A 338 TYR 0.010 0.001 TYR A 233 ARG 0.003 0.000 ARG E 321 *********************** 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 153 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7398 (t) cc_final: 0.7031 (p) REVERT: A 82 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6930 (ttmm) REVERT: A 344 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5748 (mp0) REVERT: A 396 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: A 438 ASP cc_start: 0.7594 (m-30) cc_final: 0.7258 (m-30) REVERT: C 382 ASN cc_start: 0.7946 (t0) cc_final: 0.7630 (t0) REVERT: E 139 CYS cc_start: 0.7137 (m) cc_final: 0.6837 (m) REVERT: E 242 ILE cc_start: 0.8132 (mt) cc_final: 0.7840 (mp) REVERT: E 261 ARG cc_start: 0.7007 (mmt90) cc_final: 0.6084 (ptt180) outliers start: 28 outliers final: 12 residues processed: 142 average time/residue: 1.1723 time to fit residues: 183.1135 Evaluate side-chains 131 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS 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 45 SER Chi-restraints excluded: chain C residue 110 SER 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=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: 1.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 211 GLN A 454 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN E 296 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13281 Z= 0.428 Angle : 0.668 13.953 18027 Z= 0.340 Chirality : 0.047 0.243 2082 Planarity : 0.005 0.052 2357 Dihedral : 5.927 52.656 2312 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.43 % Allowed : 14.41 % Favored : 83.16 % 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: -0.46 (0.20), residues: 1448 helix: 1.56 (0.26), residues: 355 sheet: -1.01 (0.27), residues: 273 loop : -0.89 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.002 HIS A 17 PHE 0.015 0.002 PHE E 125 TYR 0.014 0.002 TYR C 161 ARG 0.006 0.001 ARG C 150 *********************** 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 152 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7014 (ttmm) REVERT: A 189 LYS cc_start: 0.7386 (mttt) cc_final: 0.6779 (mtpm) REVERT: A 385 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 396 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: C 382 ASN cc_start: 0.8027 (t0) cc_final: 0.7734 (t0) REVERT: E 139 CYS cc_start: 0.7260 (m) cc_final: 0.6998 (m) REVERT: E 242 ILE cc_start: 0.8161 (mt) cc_final: 0.7895 (mp) REVERT: E 261 ARG cc_start: 0.7094 (mmt90) cc_final: 0.6113 (ptt180) outliers start: 31 outliers final: 13 residues processed: 142 average time/residue: 1.2506 time to fit residues: 194.1389 Evaluate side-chains 129 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 385 ILE 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 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 75 GLN A 454 GLN C 18 HIS C 341 ASN C 363 GLN E 296 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.051 13281 Z= 0.247 Angle : 0.561 12.545 18027 Z= 0.288 Chirality : 0.043 0.234 2082 Planarity : 0.004 0.048 2357 Dihedral : 5.483 46.392 2312 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.19 % Allowed : 15.19 % Favored : 82.62 % 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: -0.31 (0.20), residues: 1448 helix: 1.83 (0.26), residues: 353 sheet: -0.97 (0.27), residues: 274 loop : -0.83 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS C 18 PHE 0.011 0.001 PHE E 125 TYR 0.010 0.002 TYR A 233 ARG 0.007 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 148 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7420 (t) cc_final: 0.7042 (p) REVERT: A 82 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6988 (ttmm) REVERT: A 312 ASN cc_start: 0.7647 (t0) cc_final: 0.7389 (p0) REVERT: A 396 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: A 438 ASP cc_start: 0.7574 (m-30) cc_final: 0.7191 (m-30) REVERT: C 382 ASN cc_start: 0.7950 (t0) cc_final: 0.7679 (t0) REVERT: E 50 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7695 (mt-10) REVERT: E 139 CYS cc_start: 0.7231 (m) cc_final: 0.6945 (m) REVERT: E 242 ILE cc_start: 0.8149 (mt) cc_final: 0.7868 (mp) REVERT: E 261 ARG cc_start: 0.7027 (mmt90) cc_final: 0.6076 (ptt180) REVERT: E 401 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6506 (pm20) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 1.1700 time to fit residues: 176.8049 Evaluate side-chains 135 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS 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 18 HIS 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 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: 4.9990 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.0270 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- 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 75 GLN C 18 HIS C 341 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13281 Z= 0.362 Angle : 0.624 13.382 18027 Z= 0.318 Chirality : 0.045 0.273 2082 Planarity : 0.005 0.050 2357 Dihedral : 5.781 51.258 2312 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.96 % Allowed : 15.19 % Favored : 82.85 % 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: -0.43 (0.20), residues: 1448 helix: 1.70 (0.26), residues: 355 sheet: -1.04 (0.27), residues: 274 loop : -0.90 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS C 17 PHE 0.014 0.002 PHE E 125 TYR 0.012 0.002 TYR C 161 ARG 0.006 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 142 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7039 (ttmm) REVERT: A 312 ASN cc_start: 0.7653 (t0) cc_final: 0.7408 (p0) REVERT: A 396 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: C 382 ASN cc_start: 0.8005 (t0) cc_final: 0.7717 (t0) REVERT: E 139 CYS cc_start: 0.7248 (m) cc_final: 0.6983 (m) REVERT: E 242 ILE cc_start: 0.8175 (mt) cc_final: 0.7902 (mp) REVERT: E 261 ARG cc_start: 0.7070 (mmt90) cc_final: 0.6079 (ptt180) REVERT: E 401 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6525 (pm20) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 1.1785 time to fit residues: 174.0639 Evaluate side-chains 126 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS 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 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 101 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 75 GLN A 497 ASN C 18 HIS C 341 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13281 Z= 0.182 Angle : 0.522 11.537 18027 Z= 0.270 Chirality : 0.042 0.248 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.256 52.884 2312 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.64 % Allowed : 15.43 % Favored : 82.93 % 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 (0.21), residues: 1448 helix: 2.04 (0.26), residues: 353 sheet: -0.92 (0.27), residues: 280 loop : -0.76 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.004 0.001 HIS A 18 PHE 0.012 0.001 PHE E 353 TYR 0.011 0.001 TYR A 233 ARG 0.005 0.000 ARG A 261 ********************** 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 149 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7382 (t) cc_final: 0.7059 (p) REVERT: A 82 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6944 (ttmm) REVERT: A 114 SER cc_start: 0.7130 (t) cc_final: 0.6589 (p) REVERT: A 312 ASN cc_start: 0.7606 (t0) cc_final: 0.7365 (p0) REVERT: C 382 ASN cc_start: 0.7980 (t0) cc_final: 0.7670 (t0) REVERT: C 462 MET cc_start: 0.7335 (mtp) cc_final: 0.7131 (mtm) REVERT: E 139 CYS cc_start: 0.7121 (m) cc_final: 0.6833 (m) REVERT: E 242 ILE cc_start: 0.8137 (mt) cc_final: 0.7844 (mp) REVERT: E 261 ARG cc_start: 0.7018 (mmt90) cc_final: 0.6037 (ptt180) REVERT: E 401 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6397 (pm20) outliers start: 21 outliers final: 12 residues processed: 138 average time/residue: 1.2635 time to fit residues: 190.8431 Evaluate side-chains 130 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 402 VAL 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 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 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 75 GLN C 18 HIS C 341 ASN C 363 GLN C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.161143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141743 restraints weight = 15425.798| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.64 r_work: 0.3504 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13281 Z= 0.351 Angle : 0.625 13.026 18027 Z= 0.319 Chirality : 0.046 0.410 2082 Planarity : 0.005 0.048 2357 Dihedral : 5.737 57.157 2312 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.64 % Allowed : 15.97 % Favored : 82.38 % 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: -0.37 (0.21), residues: 1448 helix: 1.75 (0.26), residues: 357 sheet: -1.03 (0.27), residues: 274 loop : -0.86 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.009 0.001 HIS A 17 PHE 0.014 0.002 PHE E 125 TYR 0.012 0.002 TYR C 161 ARG 0.006 0.001 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.10 seconds wall clock time: 75 minutes 45.09 seconds (4545.09 seconds total)