Starting phenix.real_space_refine on Tue Aug 6 17:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/08_2024/8tp9_41470.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/08_2024/8tp9_41470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/08_2024/8tp9_41470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/08_2024/8tp9_41470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/08_2024/8tp9_41470.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/08_2024/8tp9_41470.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 87 5.16 5 C 10740 2.51 5 N 2934 2.21 5 O 3357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17118 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" 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: "J" 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: "K" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.99, per 1000 atoms: 0.58 Number of scatterers: 17118 At special positions: 0 Unit cell: (128.8, 129.95, 146.05, 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 87 16.00 O 3357 8.00 N 2934 7.00 C 10740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.01 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 501 " - " ASN A 483 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 289 " " NAG B 501 " - " ASN B 483 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 289 " " NAG C 501 " - " ASN C 483 " " NAG C 502 " - " ASN C 33 " " NAG C 503 " - " ASN C 289 " " NAG I 1 " - " ASN A 169 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN C 169 " Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 3.2 seconds 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 18.3% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 403 through 456 Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 403 through 456 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 403 through 456 Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS A 117 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS B 117 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS C 117 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 168 Processing sheet with id=AD6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR D 35 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.079A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR E 35 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.080A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.079A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 1863 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: 6.31 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4168 1.32 - 1.46: 5445 1.46 - 1.60: 7741 1.60 - 1.73: 31 1.73 - 1.87: 120 Bond restraints: 17505 Sorted by residual: bond pdb=" CB HIS B 354 " pdb=" CG HIS B 354 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CG MET B 151 " pdb=" SD MET B 151 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.26e+01 bond pdb=" CG MET C 151 " pdb=" SD MET C 151 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.25e+01 ... (remaining 17500 not shown) Histogram of bond angle deviations from ideal: 98.07 - 110.59: 5612 110.59 - 123.11: 16483 123.11 - 135.63: 1623 135.63 - 148.15: 0 148.15 - 160.67: 3 Bond angle restraints: 23721 Sorted by residual: angle pdb=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 124.56 160.67 -36.11 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C2 NAG K 1 " pdb=" N2 NAG K 1 " pdb=" C7 NAG K 1 " ideal model delta sigma weight residual 124.56 160.66 -36.10 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.64 -36.08 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N THR C 318 " pdb=" CA THR C 318 " pdb=" C THR C 318 " ideal model delta sigma weight residual 114.56 103.34 11.22 1.27e+00 6.20e-01 7.80e+01 angle pdb=" N THR B 318 " pdb=" CA THR B 318 " pdb=" C THR B 318 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 ... (remaining 23716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 10196 17.52 - 35.04: 299 35.04 - 52.56: 64 52.56 - 70.09: 61 70.09 - 87.61: 15 Dihedral angle restraints: 10635 sinusoidal: 4503 harmonic: 6132 Sorted by residual: dihedral pdb=" C TRP C 84 " pdb=" N TRP C 84 " pdb=" CA TRP C 84 " pdb=" CB TRP C 84 " ideal model delta harmonic sigma weight residual -122.60 -108.36 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TRP B 84 " pdb=" N TRP B 84 " pdb=" CA TRP B 84 " pdb=" CB TRP B 84 " ideal model delta harmonic sigma weight residual -122.60 -108.36 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TRP A 84 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " pdb=" CB TRP A 84 " ideal model delta harmonic sigma weight residual -122.60 -108.39 -14.21 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 10632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1764 0.092 - 0.183: 596 0.183 - 0.275: 156 0.275 - 0.367: 49 0.367 - 0.458: 24 Chirality restraints: 2589 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 ... (remaining 2586 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 84 " 0.102 2.00e-02 2.50e+03 4.84e-02 5.86e+01 pdb=" CG TRP B 84 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 84 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 84 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP B 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 84 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 84 " 0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 84 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 84 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 84 " -0.102 2.00e-02 2.50e+03 4.84e-02 5.85e+01 pdb=" CG TRP A 84 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 84 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 84 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP A 84 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 84 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 84 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 84 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 84 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 84 " 0.102 2.00e-02 2.50e+03 4.84e-02 5.85e+01 pdb=" CG TRP C 84 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 84 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 84 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP C 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP C 84 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 84 " 0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 84 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 84 " 0.044 2.00e-02 2.50e+03 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 5343 2.85 - 3.36: 15237 3.36 - 3.87: 29165 3.87 - 4.39: 35114 4.39 - 4.90: 57536 Nonbonded interactions: 142395 Sorted by model distance: nonbonded pdb=" O ALA B 336 " pdb=" NE1 TRP B 343 " model vdw 2.334 3.120 nonbonded pdb=" O ALA C 336 " pdb=" NE1 TRP C 343 " model vdw 2.384 3.120 nonbonded pdb=" N THR C 318 " pdb=" N GLY C 319 " model vdw 2.414 2.560 nonbonded pdb=" N THR B 318 " pdb=" N GLY B 319 " model vdw 2.414 2.560 nonbonded pdb=" N THR A 318 " pdb=" N GLY A 319 " model vdw 2.415 2.560 ... (remaining 142390 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.590 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.700 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.020 0.155 17505 Z= 1.330 Angle : 1.818 36.106 23721 Z= 1.203 Chirality : 0.108 0.458 2589 Planarity : 0.008 0.048 3057 Dihedral : 10.910 87.607 6663 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.33 % 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: 0.64 (0.17), residues: 2118 helix: 0.41 (0.24), residues: 327 sheet: 0.99 (0.22), residues: 456 loop : 0.33 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.010 TRP B 84 HIS 0.019 0.003 HIS C 18 PHE 0.036 0.006 PHE C 118 TYR 0.062 0.008 TYR D 50 ARG 0.007 0.001 ARG C 262A *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7585 (pt0) cc_final: 0.7262 (pt0) REVERT: A 268 MET cc_start: 0.7967 (ttm) cc_final: 0.7584 (ttm) REVERT: A 456 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6325 (ptt-90) REVERT: B 15 ILE cc_start: 0.8334 (mt) cc_final: 0.8119 (mt) REVERT: B 276 ASN cc_start: 0.8370 (t0) cc_final: 0.7983 (t0) REVERT: B 456 ARG cc_start: 0.7693 (mtt180) cc_final: 0.6281 (ptt-90) REVERT: C 125 LYS cc_start: 0.7445 (pttt) cc_final: 0.7225 (ptpt) REVERT: C 276 ASN cc_start: 0.8157 (t0) cc_final: 0.7752 (t0) REVERT: C 456 ARG cc_start: 0.7410 (mtt180) cc_final: 0.7093 (mtm110) REVERT: D 105 GLN cc_start: 0.6669 (mp10) cc_final: 0.6437 (pm20) REVERT: G 7 SER cc_start: 0.5669 (t) cc_final: 0.5468 (m) REVERT: G 45 LYS cc_start: 0.7486 (tttt) cc_final: 0.7280 (tttp) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.3276 time to fit residues: 214.4709 Evaluate side-chains 250 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 110 HIS A 196 GLN A 197 ASN A 410 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 197 ASN B 424 ASN B 471 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 424 ASN C 471 HIS F 27 HIS F 34 ASN F 89 GLN G 27 HIS L 27 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17505 Z= 0.267 Angle : 0.708 11.400 23721 Z= 0.378 Chirality : 0.047 0.253 2589 Planarity : 0.004 0.045 3057 Dihedral : 6.255 66.139 2649 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.61 % Allowed : 7.19 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.17), residues: 2118 helix: 1.86 (0.27), residues: 321 sheet: 0.42 (0.21), residues: 558 loop : -0.11 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 84 HIS 0.009 0.001 HIS A 355 PHE 0.020 0.003 PHE C 439 TYR 0.026 0.002 TYR A 105 ARG 0.004 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7836 (pt0) cc_final: 0.7460 (pt0) REVERT: A 147 PHE cc_start: 0.7833 (t80) cc_final: 0.7604 (t80) REVERT: A 268 MET cc_start: 0.7980 (ttm) cc_final: 0.7249 (ttm) REVERT: A 412 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7822 (mtmt) REVERT: A 456 ARG cc_start: 0.7347 (mtt180) cc_final: 0.7071 (mtm110) REVERT: B 176 MET cc_start: 0.8043 (ttm) cc_final: 0.7785 (ttm) REVERT: C 151 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7339 (mmt) REVERT: C 276 ASN cc_start: 0.8123 (t0) cc_final: 0.7859 (t0) REVERT: C 379 ASN cc_start: 0.8278 (m-40) cc_final: 0.8052 (m110) REVERT: L 61 ARG cc_start: 0.7467 (ptt-90) cc_final: 0.7226 (ptt-90) outliers start: 30 outliers final: 12 residues processed: 313 average time/residue: 0.3296 time to fit residues: 154.2838 Evaluate side-chains 248 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 354 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 244 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN D 39 GLN E 39 GLN F 38 GLN G 38 GLN H 39 GLN L 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17505 Z= 0.324 Angle : 0.676 10.923 23721 Z= 0.355 Chirality : 0.046 0.221 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.970 61.087 2649 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.36 % Allowed : 9.50 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.17), residues: 2118 helix: 1.61 (0.27), residues: 327 sheet: -0.08 (0.21), residues: 570 loop : -0.31 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 153 HIS 0.009 0.002 HIS A 355 PHE 0.027 0.002 PHE C 147 TYR 0.022 0.002 TYR B 105 ARG 0.005 0.001 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 267 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7926 (pt0) cc_final: 0.7582 (pt0) REVERT: A 268 MET cc_start: 0.7976 (ttm) cc_final: 0.7427 (ttm) REVERT: A 456 ARG cc_start: 0.7464 (mtt180) cc_final: 0.7120 (mtm110) REVERT: B 176 MET cc_start: 0.8211 (ttm) cc_final: 0.7870 (ttm) REVERT: C 151 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7795 (mmt) REVERT: C 379 ASN cc_start: 0.8383 (m-40) cc_final: 0.8138 (m110) REVERT: C 419 ASP cc_start: 0.8224 (m-30) cc_final: 0.7841 (m-30) REVERT: E 46 GLU cc_start: 0.7270 (tt0) cc_final: 0.6961 (pm20) REVERT: G 61 ARG cc_start: 0.7060 (ptp90) cc_final: 0.6843 (ptt-90) REVERT: L 89 GLN cc_start: 0.7453 (tt0) cc_final: 0.7097 (tt0) outliers start: 44 outliers final: 29 residues processed: 289 average time/residue: 0.2969 time to fit residues: 127.7283 Evaluate side-chains 254 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 224 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 chunk 191 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 181 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN B 479 ASN C 110 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17505 Z= 0.205 Angle : 0.592 10.724 23721 Z= 0.309 Chirality : 0.044 0.321 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.745 56.725 2649 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.09 % Allowed : 11.06 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.11 (0.17), residues: 2118 helix: 1.47 (0.27), residues: 345 sheet: -0.12 (0.22), residues: 540 loop : -0.46 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 153 HIS 0.006 0.001 HIS A 355 PHE 0.017 0.002 PHE A 147 TYR 0.030 0.002 TYR A 105 ARG 0.004 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 254 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7961 (pt0) cc_final: 0.7620 (pt0) REVERT: A 268 MET cc_start: 0.7948 (ttm) cc_final: 0.7386 (ttm) REVERT: A 412 LYS cc_start: 0.8285 (tmtt) cc_final: 0.7797 (mtmt) REVERT: A 456 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7010 (mtm110) REVERT: B 84 TRP cc_start: 0.8014 (OUTLIER) cc_final: 0.7469 (m-10) REVERT: B 176 MET cc_start: 0.8225 (ttm) cc_final: 0.7940 (ttm) REVERT: C 151 MET cc_start: 0.8031 (mtt) cc_final: 0.7514 (mmt) REVERT: C 379 ASN cc_start: 0.8430 (m-40) cc_final: 0.8181 (m110) REVERT: C 419 ASP cc_start: 0.8186 (m-30) cc_final: 0.7805 (m-30) REVERT: E 46 GLU cc_start: 0.7274 (tt0) cc_final: 0.6939 (pm20) REVERT: E 72 GLU cc_start: 0.7334 (mp0) cc_final: 0.7084 (mp0) REVERT: G 89 GLN cc_start: 0.7262 (tm-30) cc_final: 0.6823 (tm-30) REVERT: H 108 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8017 (tp) outliers start: 39 outliers final: 24 residues processed: 280 average time/residue: 0.2877 time to fit residues: 121.4242 Evaluate side-chains 246 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 17505 Z= 0.525 Angle : 0.780 12.869 23721 Z= 0.401 Chirality : 0.050 0.186 2589 Planarity : 0.005 0.043 3057 Dihedral : 6.151 48.627 2649 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.33 % Allowed : 11.22 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.85 (0.17), residues: 2118 helix: 1.05 (0.27), residues: 345 sheet: -0.69 (0.20), residues: 567 loop : -0.96 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 69 HIS 0.011 0.003 HIS A 184 PHE 0.023 0.003 PHE B 439 TYR 0.031 0.003 TYR G 49 ARG 0.008 0.001 ARG A 262A *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8311 (ttp) cc_final: 0.7997 (ttp) REVERT: B 84 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: B 176 MET cc_start: 0.8442 (ttm) cc_final: 0.8124 (ttm) REVERT: C 151 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8014 (mmt) REVERT: C 419 ASP cc_start: 0.8231 (m-30) cc_final: 0.7937 (m-30) REVERT: E 46 GLU cc_start: 0.7302 (tt0) cc_final: 0.6878 (pm20) outliers start: 62 outliers final: 45 residues processed: 283 average time/residue: 0.3147 time to fit residues: 131.7203 Evaluate side-chains 268 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.7980 chunk 182 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 106 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 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17505 Z= 0.201 Angle : 0.594 11.383 23721 Z= 0.309 Chirality : 0.043 0.198 2589 Planarity : 0.004 0.035 3057 Dihedral : 5.652 44.432 2649 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.52 % Allowed : 12.72 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2118 helix: 1.35 (0.27), residues: 345 sheet: -0.56 (0.21), residues: 558 loop : -0.89 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 153 HIS 0.005 0.001 HIS A 355 PHE 0.014 0.002 PHE A 439 TYR 0.025 0.002 TYR C 105 ARG 0.007 0.000 ARG L 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7932 (ttm) cc_final: 0.7246 (ttm) REVERT: A 456 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.6549 (mtm110) REVERT: B 176 MET cc_start: 0.8292 (ttm) cc_final: 0.7962 (ttm) REVERT: B 478 MET cc_start: 0.7835 (mmm) cc_final: 0.7573 (mmt) REVERT: C 88 MET cc_start: 0.8185 (ttp) cc_final: 0.7925 (ttp) REVERT: C 151 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7851 (mmt) REVERT: C 419 ASP cc_start: 0.8201 (m-30) cc_final: 0.7808 (m-30) REVERT: E 46 GLU cc_start: 0.7237 (tt0) cc_final: 0.6857 (pm20) REVERT: H 108 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (tp) outliers start: 47 outliers final: 32 residues processed: 269 average time/residue: 0.2942 time to fit residues: 118.8753 Evaluate side-chains 251 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 217 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 197 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 17505 Z= 0.456 Angle : 0.734 13.818 23721 Z= 0.377 Chirality : 0.048 0.213 2589 Planarity : 0.005 0.042 3057 Dihedral : 5.940 48.992 2649 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.44 % Allowed : 11.76 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2118 helix: 1.07 (0.27), residues: 345 sheet: -0.87 (0.21), residues: 561 loop : -1.13 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 69 HIS 0.010 0.002 HIS A 184 PHE 0.021 0.002 PHE B 439 TYR 0.025 0.003 TYR G 49 ARG 0.009 0.001 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 235 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.6679 (mtm110) REVERT: B 84 TRP cc_start: 0.8187 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: B 176 MET cc_start: 0.8448 (ttm) cc_final: 0.8140 (ttm) REVERT: B 478 MET cc_start: 0.7926 (mmm) cc_final: 0.7600 (mmt) REVERT: C 151 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7981 (mmt) REVERT: C 419 ASP cc_start: 0.8200 (m-30) cc_final: 0.7862 (m-30) REVERT: D 105 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: E 105 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7361 (pm20) outliers start: 64 outliers final: 44 residues processed: 275 average time/residue: 0.2993 time to fit residues: 122.2839 Evaluate side-chains 275 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 0.0040 chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17505 Z= 0.209 Angle : 0.595 12.215 23721 Z= 0.306 Chirality : 0.044 0.211 2589 Planarity : 0.004 0.039 3057 Dihedral : 5.561 45.354 2649 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.36 % Allowed : 12.67 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.81 (0.17), residues: 2118 helix: 1.32 (0.27), residues: 345 sheet: -0.70 (0.21), residues: 555 loop : -1.00 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 47 HIS 0.004 0.001 HIS A 355 PHE 0.013 0.002 PHE A 439 TYR 0.023 0.002 TYR C 105 ARG 0.010 0.000 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 243 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7929 (ttm) cc_final: 0.7199 (ttm) REVERT: A 456 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.6711 (mtm110) REVERT: B 176 MET cc_start: 0.8293 (ttm) cc_final: 0.7972 (ttm) REVERT: B 478 MET cc_start: 0.7837 (mmm) cc_final: 0.6430 (mmt) REVERT: C 151 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7845 (mmt) REVERT: C 419 ASP cc_start: 0.8220 (m-30) cc_final: 0.7817 (m-30) REVERT: E 46 GLU cc_start: 0.7222 (tt0) cc_final: 0.6856 (pm20) REVERT: E 105 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: F 54 LEU cc_start: 0.8222 (mm) cc_final: 0.7921 (tp) REVERT: H 108 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8061 (tp) outliers start: 44 outliers final: 32 residues processed: 270 average time/residue: 0.2953 time to fit residues: 119.4936 Evaluate side-chains 267 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 232 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 0.0010 chunk 113 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17505 Z= 0.229 Angle : 0.612 19.734 23721 Z= 0.311 Chirality : 0.044 0.199 2589 Planarity : 0.004 0.035 3057 Dihedral : 5.425 43.714 2649 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.31 % Allowed : 13.26 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.75 (0.17), residues: 2118 helix: 1.39 (0.27), residues: 345 sheet: -0.61 (0.22), residues: 555 loop : -0.99 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 47 HIS 0.005 0.001 HIS C 18 PHE 0.015 0.002 PHE C 439 TYR 0.021 0.002 TYR C 105 ARG 0.009 0.000 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7938 (ttm) cc_final: 0.7215 (ttm) REVERT: A 412 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7642 (mtpp) REVERT: A 456 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.6522 (mtm110) REVERT: B 176 MET cc_start: 0.8288 (ttm) cc_final: 0.7976 (ttm) REVERT: B 478 MET cc_start: 0.7845 (mmm) cc_final: 0.6491 (mmt) REVERT: C 151 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7567 (mmm) REVERT: C 419 ASP cc_start: 0.8199 (m-30) cc_final: 0.7779 (m-30) REVERT: E 46 GLU cc_start: 0.7221 (tt0) cc_final: 0.6850 (pm20) REVERT: E 105 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: H 108 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8063 (tp) outliers start: 43 outliers final: 35 residues processed: 269 average time/residue: 0.3237 time to fit residues: 128.8843 Evaluate side-chains 270 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 128 optimal weight: 0.0470 chunk 102 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17505 Z= 0.222 Angle : 0.595 12.200 23721 Z= 0.305 Chirality : 0.043 0.200 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.338 41.889 2649 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.15 % Allowed : 13.58 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.71 (0.18), residues: 2118 helix: 1.44 (0.27), residues: 345 sheet: -0.55 (0.22), residues: 555 loop : -0.99 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 47 HIS 0.005 0.001 HIS C 18 PHE 0.015 0.002 PHE C 439 TYR 0.027 0.002 TYR A 105 ARG 0.007 0.000 ARG G 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8441 (p) cc_final: 0.8239 (t) REVERT: A 268 MET cc_start: 0.7908 (ttm) cc_final: 0.7173 (ttm) REVERT: A 368 GLU cc_start: 0.7339 (mp0) cc_final: 0.7089 (mp0) REVERT: A 412 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7693 (mtpp) REVERT: A 456 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.6505 (mtm110) REVERT: B 176 MET cc_start: 0.8285 (ttm) cc_final: 0.7976 (ttm) REVERT: B 478 MET cc_start: 0.7836 (mmm) cc_final: 0.6507 (mmt) REVERT: C 151 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7917 (mmt) REVERT: C 419 ASP cc_start: 0.8190 (m-30) cc_final: 0.7859 (m-30) REVERT: E 46 GLU cc_start: 0.7248 (tt0) cc_final: 0.6850 (pm20) REVERT: E 105 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: H 108 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8060 (tp) outliers start: 40 outliers final: 33 residues processed: 265 average time/residue: 0.3235 time to fit residues: 127.7339 Evaluate side-chains 269 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.170278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142798 restraints weight = 21892.916| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.01 r_work: 0.3597 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17505 Z= 0.262 Angle : 0.613 12.745 23721 Z= 0.314 Chirality : 0.044 0.202 2589 Planarity : 0.004 0.035 3057 Dihedral : 5.359 41.823 2649 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.09 % Allowed : 13.85 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.76 (0.18), residues: 2118 helix: 1.39 (0.27), residues: 345 sheet: -0.59 (0.22), residues: 555 loop : -1.02 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.005 0.001 HIS A 18 PHE 0.016 0.002 PHE A 439 TYR 0.018 0.002 TYR C 105 ARG 0.007 0.001 ARG G 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.45 seconds wall clock time: 72 minutes 15.19 seconds (4335.19 seconds total)