Starting phenix.real_space_refine on Sun Jul 21 03:50:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/07_2024/8ut7_42532.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/07_2024/8ut7_42532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/07_2024/8ut7_42532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/07_2024/8ut7_42532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/07_2024/8ut7_42532.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/07_2024/8ut7_42532.cif" } resolution = 2.7 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= 0.027 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 Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" 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: 8.40, per 1000 atoms: 0.64 Number of scatterers: 13046 At special positions: 0 Unit cell: (116, 91.35, 140.65, 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=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.02 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " 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=1.17 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 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=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.89 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: 5.07 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 41 sheets defined 28.6% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 108 through 113 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: 3.903A 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: 4.831A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 404 through 456 Processing helix chain 'A' and resid 474 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: 3.847A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (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: 3.737A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.924A 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 removed outlier: 3.633A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) 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 removed outlier: 5.007A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.843A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.456A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB1, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.017A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.628A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.969A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.729A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.623A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB8, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.278A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 366 removed outlier: 4.469A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.012A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.667A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.094A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.094A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.477A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.309A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 305 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 361 through 365 Processing sheet with id=AD4, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD5, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD7, 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=AD8, first strand: chain 'E' and resid 100 through 101 removed outlier: 4.918A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.708A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AE2, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.607A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE4, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.344A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 303 through 304 613 hydrogen bonds defined for protein. 1638 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: 4.59 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4497 1.37 - 1.51: 3755 1.51 - 1.66: 4957 1.66 - 1.80: 43 1.80 - 1.95: 29 Bond restraints: 13281 Sorted by residual: bond pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " ideal model delta sigma weight residual 1.808 1.946 -0.138 3.30e-02 9.18e+02 1.76e+01 bond pdb=" N CYS E 477 " pdb=" CA CYS E 477 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.77e+00 bond pdb=" N ASP E 474 " pdb=" CA ASP E 474 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.39e+00 bond pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ASN C 278 " pdb=" CA ASN C 278 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.88e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.22: 528 107.22 - 113.92: 7229 113.92 - 120.62: 5244 120.62 - 127.32: 4874 127.32 - 134.02: 152 Bond angle restraints: 18027 Sorted by residual: angle pdb=" C PRO C 324 " pdb=" N GLU C 325 " pdb=" CA GLU C 325 " ideal model delta sigma weight residual 121.70 129.64 -7.94 1.80e+00 3.09e-01 1.94e+01 angle pdb=" CA ALA E 476 " pdb=" C ALA E 476 " pdb=" O ALA E 476 " ideal model delta sigma weight residual 120.55 116.05 4.50 1.06e+00 8.90e-01 1.80e+01 angle pdb=" CG ARG C 321 " pdb=" CD ARG C 321 " pdb=" NE ARG C 321 " ideal model delta sigma weight residual 112.00 120.90 -8.90 2.20e+00 2.07e-01 1.64e+01 angle pdb=" C ARG A 456 " pdb=" CA ARG A 456 " pdb=" CB ARG A 456 " ideal model delta sigma weight residual 117.23 111.73 5.50 1.36e+00 5.41e-01 1.64e+01 angle pdb=" C CYS C 52 " pdb=" CA CYS C 52 " pdb=" CB CYS C 52 " ideal model delta sigma weight residual 109.53 116.11 -6.58 1.65e+00 3.67e-01 1.59e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 7808 16.99 - 33.99: 326 33.99 - 50.98: 131 50.98 - 67.98: 51 67.98 - 84.97: 14 Dihedral angle restraints: 8330 sinusoidal: 3421 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " pdb=" CB CYS E 76 " ideal model delta sinusoidal sigma weight residual -86.00 -125.47 39.47 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA CYS A 97 " pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " ideal model delta sinusoidal sigma weight residual 79.00 3.13 75.87 1 2.00e+01 2.50e-03 1.81e+01 dihedral pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " ideal model delta sinusoidal sigma weight residual -73.00 -1.24 -71.76 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1280 0.044 - 0.088: 523 0.088 - 0.132: 206 0.132 - 0.176: 63 0.176 - 0.220: 10 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG E 604 " pdb=" ND2 ASN E 246 " pdb=" C2 NAG E 604 " pdb=" O5 NAG E 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+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 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA UNK G 99 " pdb=" N UNK G 99 " pdb=" C UNK G 99 " pdb=" CB UNK G 99 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 477 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C CYS E 477 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS E 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE E 478 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 74 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO A 74 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO A 74 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 75 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 69 " -0.014 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C UNK H 69 " 0.052 2.00e-02 2.50e+03 pdb=" O UNK H 69 " -0.020 2.00e-02 2.50e+03 pdb=" N UNK H 70 " -0.018 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 774 2.72 - 3.26: 12217 3.26 - 3.81: 21787 3.81 - 4.35: 27954 4.35 - 4.90: 46493 Nonbonded interactions: 109225 Sorted by model distance: nonbonded pdb=" O GLY E 218 " pdb=" NH1 ARG E 220 " model vdw 2.173 2.520 nonbonded pdb=" OE2 GLU A 401 " pdb=" CD ARG E 208 " model vdw 2.181 3.440 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG A 499 " model vdw 2.297 2.520 nonbonded pdb=" OG SER A 110 " pdb=" OD2 ASP C 408 " model vdw 2.306 2.440 ... (remaining 109220 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.450 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 0.138 13281 Z= 0.409 Angle : 1.096 12.682 18027 Z= 0.609 Chirality : 0.057 0.220 2082 Planarity : 0.006 0.046 2357 Dihedral : 12.342 84.973 5106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % 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: 0.80 (0.19), residues: 1448 helix: 1.57 (0.23), residues: 354 sheet: 0.56 (0.27), residues: 302 loop : 0.13 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP E 127 HIS 0.010 0.002 HIS A 156 PHE 0.019 0.003 PHE A 353 TYR 0.021 0.004 TYR C 195 ARG 0.019 0.002 ARG A 499 *********************** 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 163 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8410 (p) cc_final: 0.8035 (m) REVERT: A 380 LYS cc_start: 0.7506 (mtmm) cc_final: 0.6866 (mtmm) REVERT: A 401 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6714 (mm-30) REVERT: A 432 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 104 ASP cc_start: 0.8019 (t0) cc_final: 0.7731 (t0) REVERT: C 356 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7296 (tp40) REVERT: C 367 LEU cc_start: 0.8686 (mt) cc_final: 0.8193 (mt) REVERT: C 383 ARG cc_start: 0.7552 (ptm-80) cc_final: 0.6644 (ptt90) REVERT: C 498 ASN cc_start: 0.8090 (m-40) cc_final: 0.7887 (m110) REVERT: E 75 GLN cc_start: 0.7712 (mt0) cc_final: 0.7484 (mt0) REVERT: E 344 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7385 (mp0) REVERT: E 359 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6971 (mt-10) REVERT: E 475 ASN cc_start: 0.7367 (m-40) cc_final: 0.6820 (m110) outliers start: 0 outliers final: 1 residues processed: 163 average time/residue: 1.3736 time to fit residues: 243.3674 Evaluate side-chains 136 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 197 GLN A 355 HIS A 454 GLN C 122 ASN C 158 ASN C 407 GLN C 435 HIS C 454 GLN E 435 HIS E 488 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13281 Z= 0.237 Angle : 0.586 8.079 18027 Z= 0.310 Chirality : 0.044 0.235 2082 Planarity : 0.004 0.041 2357 Dihedral : 4.945 38.025 2314 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.96 % Allowed : 7.36 % Favored : 90.68 % 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: 0.86 (0.20), residues: 1448 helix: 2.35 (0.24), residues: 355 sheet: 0.21 (0.26), residues: 306 loop : -0.05 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.006 0.001 HIS A 393 PHE 0.014 0.002 PHE E 125 TYR 0.016 0.002 TYR A 195 ARG 0.009 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 178 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8262 (m-30) cc_final: 0.7892 (m-30) REVERT: A 144 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6857 (ptmt) REVERT: A 310 LYS cc_start: 0.8715 (mttt) cc_final: 0.8365 (mtmt) REVERT: A 346 MET cc_start: 0.7637 (ttp) cc_final: 0.7293 (ttp) REVERT: A 401 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6840 (mm-30) REVERT: A 460 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: A 474 ASP cc_start: 0.7470 (p0) cc_final: 0.7269 (p0) REVERT: C 201 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7801 (ptt90) REVERT: C 356 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7238 (tp40) REVERT: C 383 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.6870 (ptt90) REVERT: E 315 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8173 (mmtt) REVERT: E 359 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7161 (mt-10) outliers start: 25 outliers final: 7 residues processed: 164 average time/residue: 1.4588 time to fit residues: 258.1327 Evaluate side-chains 144 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 31 ASN A 197 GLN A 296 ASN A 312 ASN C 158 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN E 17 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2007 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= 0.382 Angle : 0.647 11.146 18027 Z= 0.334 Chirality : 0.046 0.253 2082 Planarity : 0.005 0.049 2357 Dihedral : 5.374 32.217 2312 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.27 % Allowed : 9.16 % Favored : 88.57 % 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 (0.20), residues: 1448 helix: 1.95 (0.26), residues: 353 sheet: -0.25 (0.27), residues: 295 loop : -0.61 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.009 0.002 HIS E 18 PHE 0.018 0.002 PHE C 338 TYR 0.015 0.002 TYR C 161 ARG 0.011 0.001 ARG A 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 170 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8343 (m-30) cc_final: 0.7919 (m-30) REVERT: A 310 LYS cc_start: 0.8708 (mttt) cc_final: 0.8299 (mtmt) REVERT: A 346 MET cc_start: 0.7870 (ttp) cc_final: 0.7409 (ttp) REVERT: A 401 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6863 (tm-30) REVERT: C 344 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6686 (mp0) REVERT: C 453 LYS cc_start: 0.8101 (mttm) cc_final: 0.7884 (mttm) REVERT: E 32 ASP cc_start: 0.6885 (t0) cc_final: 0.6580 (t70) REVERT: E 189 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7758 (mtpp) REVERT: E 201 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7926 (ttp-170) REVERT: E 359 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7194 (mt-10) REVERT: E 402 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8008 (t) REVERT: E 415 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7660 (m-30) outliers start: 29 outliers final: 9 residues processed: 159 average time/residue: 1.4619 time to fit residues: 251.0702 Evaluate side-chains 144 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 376 GLN A 389 ASN C 33 GLN C 158 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13281 Z= 0.227 Angle : 0.525 9.136 18027 Z= 0.272 Chirality : 0.042 0.228 2082 Planarity : 0.004 0.045 2357 Dihedral : 4.973 29.519 2312 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.72 % Allowed : 10.18 % Favored : 88.10 % 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: 2.12 (0.26), residues: 354 sheet: -0.37 (0.27), residues: 291 loop : -0.63 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.001 TYR A 195 ARG 0.009 0.001 ARG A 261 *********************** 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 164 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6632 (t0) cc_final: 0.5972 (m-40) REVERT: A 104 ASP cc_start: 0.8283 (m-30) cc_final: 0.7880 (m-30) REVERT: A 276 LYS cc_start: 0.8117 (mptt) cc_final: 0.7469 (ttpt) REVERT: A 310 LYS cc_start: 0.8684 (mttt) cc_final: 0.8320 (mtmt) REVERT: A 346 MET cc_start: 0.7897 (ttp) cc_final: 0.7520 (ttp) REVERT: A 401 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6848 (tm-30) REVERT: C 344 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6679 (mp0) REVERT: C 453 LYS cc_start: 0.8125 (mttm) cc_final: 0.7869 (mttm) REVERT: E 32 ASP cc_start: 0.6848 (t0) cc_final: 0.6577 (t70) REVERT: E 315 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8290 (mmtt) REVERT: E 344 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7476 (mp0) REVERT: E 359 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: E 415 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: E 461 ASP cc_start: 0.8425 (t0) cc_final: 0.8199 (t0) REVERT: E 475 ASN cc_start: 0.7354 (m-40) cc_final: 0.7018 (m110) outliers start: 22 outliers final: 9 residues processed: 156 average time/residue: 1.5210 time to fit residues: 255.6041 Evaluate side-chains 143 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER 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: 1.9990 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13281 Z= 0.263 Angle : 0.534 9.402 18027 Z= 0.275 Chirality : 0.043 0.234 2082 Planarity : 0.004 0.045 2357 Dihedral : 4.915 27.395 2312 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.72 % Allowed : 10.81 % Favored : 87.47 % 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 (0.20), residues: 1448 helix: 2.20 (0.26), residues: 354 sheet: -0.52 (0.27), residues: 295 loop : -0.64 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.002 TYR A 195 ARG 0.008 0.001 ARG A 261 *********************** 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 159 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6648 (t0) cc_final: 0.5974 (m-40) REVERT: A 104 ASP cc_start: 0.8294 (m-30) cc_final: 0.7889 (m-30) REVERT: A 276 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7531 (ttpt) REVERT: A 310 LYS cc_start: 0.8709 (mttt) cc_final: 0.8316 (mtmt) REVERT: A 346 MET cc_start: 0.7853 (ttp) cc_final: 0.7530 (ttp) REVERT: A 401 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6838 (tm-30) REVERT: C 344 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6663 (mp0) REVERT: C 453 LYS cc_start: 0.8168 (mttm) cc_final: 0.7903 (mttm) REVERT: E 32 ASP cc_start: 0.6879 (t0) cc_final: 0.6662 (t70) REVERT: E 315 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8304 (mmtt) REVERT: E 359 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7092 (mt-10) REVERT: E 415 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: E 461 ASP cc_start: 0.8460 (t0) cc_final: 0.8212 (t0) REVERT: E 501 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6306 (mt0) outliers start: 22 outliers final: 12 residues processed: 149 average time/residue: 1.5200 time to fit residues: 246.9908 Evaluate side-chains 148 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 HIS C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13281 Z= 0.290 Angle : 0.544 9.680 18027 Z= 0.279 Chirality : 0.043 0.235 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.026 29.680 2312 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.04 % Allowed : 11.20 % Favored : 86.77 % 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: 0.03 (0.20), residues: 1448 helix: 2.15 (0.26), residues: 354 sheet: -0.65 (0.27), residues: 299 loop : -0.68 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.002 TYR A 195 ARG 0.007 0.001 ARG C 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 162 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6679 (t0) cc_final: 0.5982 (m-40) REVERT: A 50 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7196 (pt0) REVERT: A 92 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7474 (mtpp) REVERT: A 104 ASP cc_start: 0.8289 (m-30) cc_final: 0.7872 (m-30) REVERT: A 276 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7546 (ttpt) REVERT: A 310 LYS cc_start: 0.8747 (mttt) cc_final: 0.8355 (mtmt) REVERT: A 346 MET cc_start: 0.7836 (ttp) cc_final: 0.7585 (ttp) REVERT: A 401 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6831 (tm-30) REVERT: C 201 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7830 (ptt90) REVERT: C 344 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6660 (mp0) REVERT: E 264 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7574 (pttt) REVERT: E 315 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8290 (mmtt) REVERT: E 356 GLN cc_start: 0.7607 (tt0) cc_final: 0.7343 (tt0) REVERT: E 415 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7655 (m-30) outliers start: 26 outliers final: 14 residues processed: 151 average time/residue: 1.4820 time to fit residues: 241.5021 Evaluate side-chains 150 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13281 Z= 0.314 Angle : 0.560 10.255 18027 Z= 0.286 Chirality : 0.043 0.239 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.189 32.534 2312 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.72 % Allowed : 12.06 % Favored : 86.22 % 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 (0.20), residues: 1448 helix: 2.09 (0.26), residues: 354 sheet: -0.63 (0.27), residues: 293 loop : -0.72 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.002 TYR A 233 ARG 0.007 0.001 ARG C 321 *********************** 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 155 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7272 (pt0) REVERT: A 92 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7465 (mtpp) REVERT: A 104 ASP cc_start: 0.8311 (m-30) cc_final: 0.7901 (m-30) REVERT: A 276 LYS cc_start: 0.8168 (mptt) cc_final: 0.7567 (ttpt) REVERT: A 310 LYS cc_start: 0.8748 (mttt) cc_final: 0.8359 (mtmt) REVERT: A 389 ASN cc_start: 0.7554 (m-40) cc_final: 0.6114 (p0) REVERT: A 401 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6833 (tm-30) REVERT: C 201 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7837 (ptt90) REVERT: C 344 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6665 (mp0) REVERT: C 401 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: E 315 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8284 (mmtt) REVERT: E 356 GLN cc_start: 0.7583 (tt0) cc_final: 0.7329 (tt0) REVERT: E 415 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: E 501 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6273 (mt0) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 1.5246 time to fit residues: 236.5761 Evaluate side-chains 149 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13281 Z= 0.315 Angle : 0.560 10.124 18027 Z= 0.287 Chirality : 0.044 0.233 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.215 33.984 2312 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.04 % Allowed : 11.90 % Favored : 86.06 % 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: -0.05 (0.20), residues: 1448 helix: 2.07 (0.26), residues: 354 sheet: -0.66 (0.27), residues: 293 loop : -0.75 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.002 TYR C 486 ARG 0.008 0.001 ARG C 321 *********************** 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 155 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7330 (pt0) REVERT: A 92 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7455 (mtpp) REVERT: A 104 ASP cc_start: 0.8315 (m-30) cc_final: 0.7904 (m-30) REVERT: A 276 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7579 (ttpt) REVERT: A 310 LYS cc_start: 0.8754 (mttt) cc_final: 0.8362 (mtmt) REVERT: A 389 ASN cc_start: 0.7562 (m-40) cc_final: 0.6122 (p0) REVERT: A 401 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6861 (tm-30) REVERT: A 475 ASN cc_start: 0.6947 (m110) cc_final: 0.6715 (m110) REVERT: C 201 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7826 (ptt90) REVERT: C 280 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: C 344 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6663 (mp0) REVERT: C 401 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: E 315 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: E 356 GLN cc_start: 0.7603 (tt0) cc_final: 0.7346 (tt0) REVERT: E 415 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: E 501 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6294 (mt0) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 1.5686 time to fit residues: 241.1715 Evaluate side-chains 149 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 5.9990 chunk 139 optimal weight: 0.0770 chunk 149 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13281 Z= 0.157 Angle : 0.473 7.469 18027 Z= 0.246 Chirality : 0.041 0.239 2082 Planarity : 0.004 0.042 2357 Dihedral : 4.638 25.003 2312 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.41 % Allowed : 12.76 % Favored : 85.83 % 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: 2.30 (0.26), residues: 355 sheet: -0.64 (0.27), residues: 299 loop : -0.60 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.002 0.001 HIS E 355 PHE 0.016 0.001 PHE C 338 TYR 0.008 0.001 TYR C 486 ARG 0.008 0.001 ARG A 142 *********************** 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 155 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7250 (pt0) REVERT: A 92 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7428 (mtpp) REVERT: A 104 ASP cc_start: 0.8239 (m-30) cc_final: 0.7850 (m-30) REVERT: A 276 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7519 (ttpt) REVERT: A 310 LYS cc_start: 0.8736 (mttt) cc_final: 0.8377 (mtmt) REVERT: A 389 ASN cc_start: 0.7469 (m-40) cc_final: 0.6119 (p0) REVERT: A 401 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6871 (tm-30) REVERT: C 280 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: C 344 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6316 (mp0) REVERT: C 401 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: E 315 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8295 (mmtt) REVERT: E 356 GLN cc_start: 0.7601 (tt0) cc_final: 0.7378 (tt0) REVERT: E 415 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7515 (t70) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 1.5918 time to fit residues: 247.9922 Evaluate side-chains 144 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13281 Z= 0.197 Angle : 0.491 8.250 18027 Z= 0.255 Chirality : 0.042 0.223 2082 Planarity : 0.004 0.043 2357 Dihedral : 4.620 23.662 2312 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.10 % Allowed : 13.08 % Favored : 85.83 % 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: 0.21 (0.20), residues: 1448 helix: 2.39 (0.26), residues: 354 sheet: -0.57 (0.27), residues: 299 loop : -0.60 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS C 393 PHE 0.013 0.001 PHE A 353 TYR 0.009 0.001 TYR C 486 ARG 0.008 0.000 ARG C 321 ********************** 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 148 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7261 (pt0) REVERT: A 92 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7451 (mtpp) REVERT: A 104 ASP cc_start: 0.8251 (m-30) cc_final: 0.7848 (m-30) REVERT: A 276 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7567 (ttpt) REVERT: A 310 LYS cc_start: 0.8734 (mttt) cc_final: 0.8378 (mtmt) REVERT: A 389 ASN cc_start: 0.7459 (m-40) cc_final: 0.6132 (p0) REVERT: A 401 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6895 (tm-30) REVERT: C 280 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 344 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6677 (mp0) REVERT: E 315 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8287 (mmtt) REVERT: E 356 GLN cc_start: 0.7590 (tt0) cc_final: 0.7355 (tt0) REVERT: E 415 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7558 (t70) outliers start: 14 outliers final: 8 residues processed: 140 average time/residue: 1.5704 time to fit residues: 236.4134 Evaluate side-chains 143 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124531 restraints weight = 13611.142| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.49 r_work: 0.3252 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13281 Z= 0.257 Angle : 0.523 8.981 18027 Z= 0.270 Chirality : 0.043 0.226 2082 Planarity : 0.004 0.043 2357 Dihedral : 4.816 26.791 2312 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.41 % Allowed : 12.61 % 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: 0.12 (0.20), residues: 1448 helix: 2.27 (0.26), residues: 354 sheet: -0.59 (0.27), residues: 299 loop : -0.65 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.018 0.001 PHE C 338 TYR 0.009 0.002 TYR C 486 ARG 0.008 0.001 ARG C 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4759.87 seconds wall clock time: 84 minutes 28.94 seconds (5068.94 seconds total)