Starting phenix.real_space_refine on Sun Mar 17 08:30:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/03_2024/8tp9_41470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/03_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_41470/03_2024/8tp9_41470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/03_2024/8tp9_41470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/03_2024/8tp9_41470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp9_41470/03_2024/8tp9_41470.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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-5265/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: 8.37, per 1000 atoms: 0.49 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: 5.92 Conformation dependent library (CDL) restraints added in 2.8 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: 2.17 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: 6.37 Time building geometry restraints manager: 6.52 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 2.520 nonbonded pdb=" O ALA C 336 " pdb=" NE1 TRP C 343 " model vdw 2.384 2.520 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 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.080 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 44.910 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.490 ------------------------------------------------------------------------------- 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 : 2.081 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: 0.3182 time to fit residues: 206.0425 Evaluate side-chains 250 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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: 0.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 196 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 371 GLN B 424 ASN B 471 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 ASN C 471 HIS D 39 GLN E 39 GLN F 27 HIS F 38 GLN G 27 HIS G 38 GLN H 39 GLN L 27 HIS L 38 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17505 Z= 0.257 Angle : 0.689 11.247 23721 Z= 0.370 Chirality : 0.046 0.215 2589 Planarity : 0.004 0.034 3057 Dihedral : 6.345 66.346 2649 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 0.45 (0.17), residues: 2118 helix: 1.89 (0.27), residues: 321 sheet: 0.39 (0.21), residues: 558 loop : -0.12 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 84 HIS 0.008 0.001 HIS A 355 PHE 0.021 0.003 PHE C 118 TYR 0.028 0.002 TYR A 105 ARG 0.003 0.000 ARG E 94 *********************** 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 331 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 301 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7701 (pt0) cc_final: 0.7316 (pt0) REVERT: A 147 PHE cc_start: 0.7821 (t80) cc_final: 0.7595 (t80) REVERT: A 412 LYS cc_start: 0.8371 (tmtt) cc_final: 0.7847 (mtmt) REVERT: A 456 ARG cc_start: 0.7316 (mtt180) cc_final: 0.7082 (mtm110) REVERT: B 12 GLN cc_start: 0.8295 (pt0) cc_final: 0.7998 (pt0) REVERT: B 176 MET cc_start: 0.8039 (ttm) cc_final: 0.7787 (ttm) REVERT: C 151 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7411 (mmt) REVERT: C 379 ASN cc_start: 0.8266 (m-40) cc_final: 0.8048 (m110) REVERT: G 61 ARG cc_start: 0.7333 (ptt-90) cc_final: 0.6784 (ptt-90) outliers start: 30 outliers final: 11 residues processed: 317 average time/residue: 0.2996 time to fit residues: 140.7786 Evaluate side-chains 250 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 238 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET 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 151 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 78 LEU 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: 0.6980 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 52 optimal weight: 0.0070 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 410 ASN C 73 ASN C 244 ASN C 371 GLN C 479 ASN F 31 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17505 Z= 0.212 Angle : 0.592 8.912 23721 Z= 0.313 Chirality : 0.044 0.232 2589 Planarity : 0.004 0.035 3057 Dihedral : 5.863 62.523 2649 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.36 % Allowed : 9.34 % Favored : 88.30 % 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: 0.34 (0.17), residues: 2118 helix: 1.86 (0.27), residues: 327 sheet: 0.21 (0.21), residues: 564 loop : -0.15 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 84 HIS 0.008 0.001 HIS A 355 PHE 0.031 0.002 PHE C 147 TYR 0.019 0.002 TYR C 105 ARG 0.005 0.000 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 317 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7887 (pt0) cc_final: 0.7524 (pt0) REVERT: A 268 MET cc_start: 0.7949 (ttm) cc_final: 0.7352 (ttm) REVERT: A 412 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7793 (mtmt) REVERT: A 456 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7196 (mtm110) REVERT: B 176 MET cc_start: 0.8139 (ttm) cc_final: 0.7853 (ttm) REVERT: B 456 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.6395 (mtm110) REVERT: C 151 MET cc_start: 0.7905 (mtt) cc_final: 0.7405 (mmt) REVERT: C 276 ASN cc_start: 0.8210 (t0) cc_final: 0.8007 (t0) REVERT: C 419 ASP cc_start: 0.8170 (m-30) cc_final: 0.7780 (m-30) REVERT: C 478 MET cc_start: 0.7217 (mmt) cc_final: 0.6891 (mmt) REVERT: E 46 GLU cc_start: 0.7239 (tt0) cc_final: 0.6961 (pm20) REVERT: G 61 ARG cc_start: 0.7138 (ptt-90) cc_final: 0.6721 (ptt-90) REVERT: H 91 TYR cc_start: 0.7874 (m-80) cc_final: 0.7646 (m-80) outliers start: 44 outliers final: 32 residues processed: 296 average time/residue: 0.2730 time to fit residues: 122.4209 Evaluate side-chains 263 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 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 77 ASP 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 77 ASP 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 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 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: 1.9990 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 0.0270 chunk 181 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- 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 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN C 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17505 Z= 0.322 Angle : 0.649 10.445 23721 Z= 0.338 Chirality : 0.045 0.208 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.865 56.481 2649 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.58 % Allowed : 10.20 % Favored : 87.22 % 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: -0.13 (0.17), residues: 2118 helix: 1.70 (0.27), residues: 327 sheet: -0.21 (0.20), residues: 591 loop : -0.48 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 343 HIS 0.008 0.002 HIS A 184 PHE 0.022 0.002 PHE B 147 TYR 0.028 0.002 TYR A 105 ARG 0.005 0.001 ARG B 262a *********************** 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 300 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7948 (pt0) cc_final: 0.7628 (pt0) REVERT: A 268 MET cc_start: 0.7916 (ttm) cc_final: 0.7262 (ttm) REVERT: A 412 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7781 (mtmt) REVERT: A 456 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7164 (mtm110) REVERT: B 84 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: B 176 MET cc_start: 0.8289 (ttm) cc_final: 0.7974 (ttm) REVERT: C 151 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7923 (mmt) REVERT: C 419 ASP cc_start: 0.8161 (m-30) cc_final: 0.7886 (m-30) REVERT: E 46 GLU cc_start: 0.7199 (tt0) cc_final: 0.6891 (pm20) REVERT: G 61 ARG cc_start: 0.7301 (ptt-90) cc_final: 0.6980 (ptt-90) REVERT: G 89 GLN cc_start: 0.7345 (tt0) cc_final: 0.6976 (tm-30) REVERT: H 35 ASN cc_start: 0.8263 (m-40) cc_final: 0.8037 (m-40) REVERT: L 61 ARG cc_start: 0.7698 (ptt-90) cc_final: 0.7445 (ptt-90) outliers start: 48 outliers final: 32 residues processed: 283 average time/residue: 0.2830 time to fit residues: 120.0497 Evaluate side-chains 262 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 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 46 THR Chi-restraints excluded: chain B residue 77 ASP 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 B residue 242 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 77 ASP 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 290 THR 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 78 LEU Chi-restraints excluded: chain E residue 108 LEU 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 25 SER Chi-restraints excluded: chain H residue 56 VAL 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: 0.5980 chunk 2 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17505 Z= 0.361 Angle : 0.670 13.116 23721 Z= 0.345 Chirality : 0.046 0.192 2589 Planarity : 0.004 0.032 3057 Dihedral : 5.873 47.331 2649 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.54 % Allowed : 11.11 % Favored : 85.35 % 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: -0.54 (0.17), residues: 2118 helix: 1.31 (0.27), residues: 345 sheet: -0.46 (0.21), residues: 564 loop : -0.77 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 47 HIS 0.007 0.002 HIS A 184 PHE 0.018 0.002 PHE C 439 TYR 0.022 0.002 TYR A 105 ARG 0.008 0.001 ARG L 103 *********************** 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 299 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7908 (ttm) cc_final: 0.7262 (ttm) REVERT: A 456 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7130 (mtm110) REVERT: B 84 TRP cc_start: 0.8097 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: B 176 MET cc_start: 0.8370 (ttm) cc_final: 0.7907 (ttm) REVERT: C 109 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8464 (mtpp) REVERT: C 151 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7878 (mmt) REVERT: C 419 ASP cc_start: 0.8140 (m-30) cc_final: 0.7834 (m-30) REVERT: G 61 ARG cc_start: 0.7384 (ptt-90) cc_final: 0.7124 (ptt-90) REVERT: H 35 ASN cc_start: 0.8346 (m-40) cc_final: 0.8055 (m-40) outliers start: 66 outliers final: 44 residues processed: 277 average time/residue: 0.2979 time to fit residues: 122.2654 Evaluate side-chains 263 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 77 ASP 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 77 ASP 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 462 LEU Chi-restraints excluded: chain C residue 77 ASP 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 109 LYS 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 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 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 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4111 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= 0.210 Angle : 0.580 11.661 23721 Z= 0.298 Chirality : 0.043 0.210 2589 Planarity : 0.004 0.031 3057 Dihedral : 5.509 44.097 2649 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.01 % Allowed : 11.86 % Favored : 85.13 % 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 (0.18), residues: 2118 helix: 1.51 (0.27), residues: 345 sheet: -0.44 (0.21), residues: 558 loop : -0.74 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 47 HIS 0.005 0.001 HIS A 355 PHE 0.016 0.002 PHE B 147 TYR 0.028 0.002 TYR A 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 290 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7891 (ttm) cc_final: 0.7176 (ttm) REVERT: A 412 LYS cc_start: 0.8303 (tmtt) cc_final: 0.7844 (mtmt) REVERT: A 456 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7292 (mtm110) REVERT: B 84 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: B 176 MET cc_start: 0.8275 (ttm) cc_final: 0.7935 (ttm) REVERT: B 321 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7505 (ptp-110) REVERT: C 151 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7856 (mmt) REVERT: C 419 ASP cc_start: 0.8146 (m-30) cc_final: 0.7827 (m-30) REVERT: C 478 MET cc_start: 0.7180 (mmt) cc_final: 0.6717 (mmt) REVERT: E 46 GLU cc_start: 0.7219 (tt0) cc_final: 0.6992 (pm20) REVERT: E 105 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: G 61 ARG cc_start: 0.7362 (ptt-90) cc_final: 0.7092 (ptt-90) REVERT: H 35 ASN cc_start: 0.8199 (m-40) cc_final: 0.7988 (m110) outliers start: 56 outliers final: 36 residues processed: 270 average time/residue: 0.2965 time to fit residues: 118.8856 Evaluate side-chains 256 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 217 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL 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 77 ASP 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 323 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 77 ASP 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 176 MET Chi-restraints excluded: chain C residue 197 ASN 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 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 F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 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: 3.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 0.0970 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17505 Z= 0.282 Angle : 0.618 13.180 23721 Z= 0.316 Chirality : 0.044 0.203 2589 Planarity : 0.004 0.033 3057 Dihedral : 5.484 43.602 2649 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.79 % Allowed : 12.24 % 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: -0.53 (0.18), residues: 2118 helix: 1.49 (0.27), residues: 345 sheet: -0.52 (0.21), residues: 555 loop : -0.79 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 47 HIS 0.006 0.002 HIS A 184 PHE 0.015 0.002 PHE C 439 TYR 0.027 0.002 TYR A 105 ARG 0.009 0.001 ARG G 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 287 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 235 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7925 (ttm) cc_final: 0.7194 (ttm) REVERT: A 412 LYS cc_start: 0.8284 (tmtt) cc_final: 0.7841 (mtmt) REVERT: A 456 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7352 (mtm110) REVERT: B 84 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: B 176 MET cc_start: 0.8351 (ttm) cc_final: 0.8031 (ttm) REVERT: B 321 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7634 (ptp-110) REVERT: C 109 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: C 151 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7944 (mmt) REVERT: C 419 ASP cc_start: 0.8154 (m-30) cc_final: 0.7914 (m-30) REVERT: E 105 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: G 61 ARG cc_start: 0.7385 (ptt-90) cc_final: 0.7112 (ptt-90) REVERT: H 35 ASN cc_start: 0.8287 (m-40) cc_final: 0.8034 (m-40) outliers start: 52 outliers final: 42 residues processed: 269 average time/residue: 0.2994 time to fit residues: 120.0559 Evaluate side-chains 275 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL 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 77 ASP 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 323 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 77 ASP 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 109 LYS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 176 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 C residue 485 THR 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 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 53 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 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 Chi-restraints excluded: chain L residue 100 GLN 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: 0.4980 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 282 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4340 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= 0.221 Angle : 0.584 12.387 23721 Z= 0.299 Chirality : 0.043 0.206 2589 Planarity : 0.004 0.035 3057 Dihedral : 5.350 41.617 2649 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.84 % Allowed : 12.61 % Favored : 84.54 % 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: -0.47 (0.18), residues: 2118 helix: 1.55 (0.27), residues: 345 sheet: -0.45 (0.21), residues: 555 loop : -0.77 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 47 HIS 0.006 0.001 HIS L 27 PHE 0.014 0.002 PHE A 439 TYR 0.029 0.002 TYR A 105 ARG 0.008 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 290 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.7934 (ttm) cc_final: 0.7204 (ttm) REVERT: A 412 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7702 (mtpp) REVERT: A 456 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7300 (mtm110) REVERT: B 176 MET cc_start: 0.8290 (ttm) cc_final: 0.7976 (ttm) REVERT: B 321 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7642 (ptp-110) REVERT: B 478 MET cc_start: 0.7839 (mmm) cc_final: 0.6817 (mmt) REVERT: C 419 ASP cc_start: 0.8128 (m-30) cc_final: 0.7869 (m-30) REVERT: C 478 MET cc_start: 0.7316 (mmt) cc_final: 0.6862 (mmt) REVERT: E 105 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: G 61 ARG cc_start: 0.7373 (ptt-90) cc_final: 0.7090 (ptt-90) REVERT: H 35 ASN cc_start: 0.8213 (m-40) cc_final: 0.7993 (m-40) outliers start: 53 outliers final: 40 residues processed: 273 average time/residue: 0.3212 time to fit residues: 132.2696 Evaluate side-chains 268 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 227 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 77 ASP 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 323 VAL 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 77 ASP 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 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 37 ILE 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 20 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4321 > 50: distance: 35 - 41: 26.490 distance: 41 - 42: 19.502 distance: 42 - 43: 22.987 distance: 42 - 45: 16.120 distance: 43 - 44: 19.816 distance: 43 - 47: 30.278 distance: 45 - 46: 14.822 distance: 46 - 161: 15.275 distance: 47 - 48: 28.299 distance: 48 - 49: 22.077 distance: 48 - 51: 15.033 distance: 49 - 50: 14.194 distance: 49 - 59: 31.485 distance: 51 - 52: 7.461 distance: 52 - 53: 8.613 distance: 52 - 54: 12.822 distance: 53 - 55: 4.832 distance: 54 - 56: 4.181 distance: 55 - 57: 6.782 distance: 56 - 57: 12.819 distance: 57 - 58: 17.687 distance: 59 - 60: 12.457 distance: 59 - 65: 17.628 distance: 60 - 61: 5.172 distance: 60 - 63: 6.367 distance: 61 - 62: 13.109 distance: 61 - 66: 18.368 distance: 63 - 64: 16.264 distance: 64 - 65: 19.111 distance: 66 - 67: 18.182 distance: 67 - 68: 40.555 distance: 68 - 69: 17.247 distance: 68 - 70: 28.911 distance: 70 - 71: 7.474 distance: 71 - 72: 17.323 distance: 71 - 74: 14.076 distance: 72 - 73: 19.400 distance: 72 - 76: 10.195 distance: 74 - 75: 11.189 distance: 76 - 77: 7.666 distance: 77 - 78: 9.699 distance: 77 - 80: 18.050 distance: 78 - 79: 26.368 distance: 78 - 87: 8.389 distance: 80 - 81: 15.028 distance: 81 - 82: 14.650 distance: 81 - 83: 8.544 distance: 82 - 84: 10.619 distance: 83 - 85: 8.510 distance: 84 - 86: 10.130 distance: 85 - 86: 10.473 distance: 87 - 88: 5.326 distance: 88 - 89: 4.373 distance: 88 - 91: 8.396 distance: 89 - 90: 4.006 distance: 89 - 95: 6.078 distance: 91 - 92: 4.958 distance: 92 - 93: 7.971 distance: 92 - 94: 11.224 distance: 95 - 96: 4.924 distance: 96 - 99: 4.967 distance: 97 - 98: 15.577 distance: 98 - 131: 19.851 distance: 99 - 100: 5.217 distance: 100 - 101: 3.182 distance: 103 - 104: 5.891 distance: 104 - 107: 5.461 distance: 105 - 106: 3.210 distance: 105 - 115: 3.298 distance: 106 - 138: 3.680 distance: 107 - 108: 4.129 distance: 108 - 109: 4.985 distance: 108 - 110: 3.664 distance: 110 - 112: 3.132 distance: 113 - 114: 3.942 distance: 116 - 117: 4.264 distance: 116 - 119: 5.623 distance: 118 - 147: 7.263 distance: 119 - 120: 7.257 distance: 120 - 121: 4.786 distance: 121 - 122: 3.885 distance: 121 - 123: 4.846