Starting phenix.real_space_refine on Tue Aug 6 19:51:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp5_41467/08_2024/8tp5_41467.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp5_41467/08_2024/8tp5_41467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp5_41467/08_2024/8tp5_41467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp5_41467/08_2024/8tp5_41467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp5_41467/08_2024/8tp5_41467.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp5_41467/08_2024/8tp5_41467.cif" } resolution = 2.9 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= 0.051 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 78 5.16 5 C 10986 2.51 5 N 2997 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 246": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "H ASP 27": "OD1" <-> "OD2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 27": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17508 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 836 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "I" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "J" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 836 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 836 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "M" 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: "N" 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: "O" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.01, per 1000 atoms: 0.57 Number of scatterers: 17508 At special positions: 0 Unit cell: (140.3, 134.55, 167.9, 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 78 16.00 O 3447 8.00 N 2997 7.00 C 10986 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 B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.07 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=2.08 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.07 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=2.08 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.07 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.08 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 63 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 63 " " NAG C 404 " - " ASN C 129 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 33 " " NAG G 403 " - " ASN G 63 " " NAG G 404 " - " ASN G 129 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN C 95 " " NAG O 1 " - " ASN G 95 " Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.6 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 51 sheets defined 21.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 170 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 'F' and resid 29 through 30C Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP G 127 " --> pdb=" O LYS G 125A" (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 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 helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) 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: 7.749A pdb=" N LEU A 51 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA A 279 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A 53 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 87 " --> pdb=" O ILE 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 115 through 122 removed outlier: 6.577A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 144 through 146 removed outlier: 9.996A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.749A pdb=" N LEU C 51 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 53 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 144 through 146 removed outlier: 9.995A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER F 2 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 98 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS F 88 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER F 2 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 98 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS F 88 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 18 through 24 Processing sheet with id=AD2, first strand: chain 'I' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS I 137 " --> pdb=" O ILE I 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'G' and resid 51 through 54 removed outlier: 7.748A pdb=" N LEU G 51 " --> pdb=" O CYS G 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA G 279 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 53 " --> pdb=" O ALA G 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 144 through 146 removed outlier: 9.995A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE3, first strand: chain 'G' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'K' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER K 2 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 98 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER K 2 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 98 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF4, first strand: chain 'L' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER L 2 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE L 98 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER L 2 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE L 98 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 24 788 hydrogen bonds defined for protein. 2043 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: 6.22 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4751 1.33 - 1.47: 5836 1.47 - 1.61: 7221 1.61 - 1.75: 21 1.75 - 1.89: 99 Bond restraints: 17928 Sorted by residual: bond pdb=" CB HIS G 47 " pdb=" CG HIS G 47 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.30e+01 bond pdb=" CB HIS A 47 " pdb=" CG HIS A 47 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.24e+01 bond pdb=" CB HIS C 47 " pdb=" CG HIS C 47 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" NE1 TRP C 127 " pdb=" CE2 TRP C 127 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.11e+01 bond pdb=" NE1 TRP A 127 " pdb=" CE2 TRP A 127 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.08e+01 ... (remaining 17923 not shown) Histogram of bond angle deviations from ideal: 96.55 - 109.50: 3510 109.50 - 122.46: 18083 122.46 - 135.42: 2722 135.42 - 148.37: 0 148.37 - 161.33: 12 Bond angle restraints: 24327 Sorted by residual: angle pdb=" C2 NAG A 403 " pdb=" N2 NAG A 403 " pdb=" C7 NAG A 403 " ideal model delta sigma weight residual 124.56 161.33 -36.77 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG G 403 " pdb=" N2 NAG G 403 " pdb=" C7 NAG G 403 " ideal model delta sigma weight residual 124.56 161.27 -36.71 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG C 403 " pdb=" N2 NAG C 403 " pdb=" C7 NAG C 403 " ideal model delta sigma weight residual 124.56 161.26 -36.70 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG G 404 " pdb=" N2 NAG G 404 " pdb=" C7 NAG G 404 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG C 404 " pdb=" N2 NAG C 404 " pdb=" C7 NAG C 404 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 ... (remaining 24322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 10408 17.37 - 34.74: 281 34.74 - 52.11: 65 52.11 - 69.49: 58 69.49 - 86.86: 18 Dihedral angle restraints: 10830 sinusoidal: 4512 harmonic: 6318 Sorted by residual: dihedral pdb=" C ASN K 29 " pdb=" N ASN K 29 " pdb=" CA ASN K 29 " pdb=" CB ASN K 29 " ideal model delta harmonic sigma weight residual -122.60 -112.41 -10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -117.95 31.95 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS G 64 " pdb=" SG CYS G 64 " pdb=" SG CYS G 76 " pdb=" CB CYS G 76 " ideal model delta sinusoidal sigma weight residual -86.00 -117.94 31.94 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 10827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1799 0.090 - 0.180: 629 0.180 - 0.270: 149 0.270 - 0.360: 54 0.360 - 0.449: 21 Chirality restraints: 2652 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.01e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.95e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.87e+01 ... (remaining 2649 not shown) Planarity restraints: 3165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 171 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLU I 171 " -0.104 2.00e-02 2.50e+03 pdb=" O GLU I 171 " 0.037 2.00e-02 2.50e+03 pdb=" OXT GLU I 171 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 171 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLU D 171 " -0.104 2.00e-02 2.50e+03 pdb=" O GLU D 171 " 0.037 2.00e-02 2.50e+03 pdb=" OXT GLU D 171 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 171 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLU B 171 " -0.104 2.00e-02 2.50e+03 pdb=" O GLU B 171 " 0.037 2.00e-02 2.50e+03 pdb=" OXT GLU B 171 " 0.037 2.00e-02 2.50e+03 ... (remaining 3162 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5676 2.85 - 3.36: 15648 3.36 - 3.87: 30444 3.87 - 4.39: 36248 4.39 - 4.90: 59564 Nonbonded interactions: 147580 Sorted by model distance: nonbonded pdb=" OD1 ASN K 29 " pdb=" CB ASP K 92 " model vdw 2.336 3.440 nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP D 85 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS D 83 " pdb=" OD1 ASP I 85 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS I 83 " model vdw 2.337 3.120 nonbonded pdb=" O SER L 26 " pdb=" O ASN L 29 " model vdw 2.396 3.040 ... (remaining 147575 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.740 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.021 0.133 17928 Z= 1.370 Angle : 1.858 36.768 24327 Z= 1.164 Chirality : 0.105 0.449 2652 Planarity : 0.009 0.060 3150 Dihedral : 10.607 86.858 6744 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.17), residues: 2181 helix: 0.69 (0.24), residues: 363 sheet: 0.96 (0.22), residues: 522 loop : 0.78 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.007 TRP I 21 HIS 0.020 0.004 HIS K 34 PHE 0.043 0.007 PHE G 118 TYR 0.062 0.009 TYR I 24 ARG 0.014 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 378 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7629 (ptmm) cc_final: 0.7140 (mmmt) REVERT: C 144 LYS cc_start: 0.7605 (ptmm) cc_final: 0.7201 (mmmt) REVERT: J 80 MET cc_start: 0.7417 (tmm) cc_final: 0.7045 (tmm) REVERT: L 30 THR cc_start: 0.7852 (p) cc_final: 0.7496 (p) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 1.2692 time to fit residues: 537.4294 Evaluate side-chains 186 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 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 190 ASN A 298 HIS A 322 ASN B 60 ASN C 18 HIS C 60 GLN C 298 HIS F 34 HIS G 18 HIS G 60 GLN G 298 HIS G 322 ASN J 100AHIS K 34 HIS L 34 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17928 Z= 0.230 Angle : 0.605 6.843 24327 Z= 0.332 Chirality : 0.046 0.181 2652 Planarity : 0.005 0.034 3150 Dihedral : 6.948 84.550 2780 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.97 % Allowed : 7.53 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.17), residues: 2181 helix: 1.87 (0.26), residues: 366 sheet: 0.75 (0.21), residues: 555 loop : 0.30 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 21 HIS 0.006 0.001 HIS E 58 PHE 0.037 0.002 PHE G 118 TYR 0.016 0.002 TYR B 22 ARG 0.006 0.001 ARG D 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7164 (p0) cc_final: 0.6808 (p0) REVERT: C 75 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: C 144 LYS cc_start: 0.7672 (ptmm) cc_final: 0.7410 (mmmt) REVERT: C 285 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7158 (mm-40) REVERT: G 285 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7010 (mm-40) REVERT: I 72 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7628 (ptmt) REVERT: J 80 MET cc_start: 0.7264 (tmm) cc_final: 0.6871 (tmm) REVERT: K 29 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8180 (m-40) outliers start: 56 outliers final: 23 residues processed: 235 average time/residue: 1.1656 time to fit residues: 309.4439 Evaluate side-chains 189 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS C 141 HIS D 26 HIS D 60 ASN F 29 ASN G 199 ASN I 26 HIS I 60 ASN K 29 ASN L 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17928 Z= 0.304 Angle : 0.602 7.053 24327 Z= 0.325 Chirality : 0.046 0.226 2652 Planarity : 0.005 0.038 3150 Dihedral : 6.075 81.855 2780 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.13 % Allowed : 9.96 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.17), residues: 2181 helix: 2.09 (0.27), residues: 366 sheet: 0.79 (0.22), residues: 564 loop : -0.04 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 36 HIS 0.010 0.002 HIS I 26 PHE 0.038 0.002 PHE A 118 TYR 0.015 0.002 TYR B 162 ARG 0.009 0.001 ARG L 95A *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 205 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8853 (m-80) cc_final: 0.8581 (m-80) REVERT: B 113 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8730 (m) REVERT: C 144 LYS cc_start: 0.7785 (ptmm) cc_final: 0.7527 (mmmt) REVERT: C 285 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7532 (mm-40) REVERT: H 61 GLN cc_start: 0.7283 (tp40) cc_final: 0.7047 (tp40) REVERT: I 72 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7628 (ptmt) REVERT: J 80 MET cc_start: 0.7726 (tmm) cc_final: 0.7261 (tmm) REVERT: J 90 TYR cc_start: 0.8462 (m-80) cc_final: 0.8256 (m-80) outliers start: 59 outliers final: 27 residues processed: 238 average time/residue: 1.1723 time to fit residues: 314.9933 Evaluate side-chains 207 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 295 GLN B 26 HIS D 26 HIS G 141 HIS G 190 ASN G 199 ASN G 295 GLN I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17928 Z= 0.424 Angle : 0.661 9.150 24327 Z= 0.350 Chirality : 0.048 0.189 2652 Planarity : 0.005 0.043 3150 Dihedral : 6.029 79.315 2780 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.66 % Allowed : 11.34 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2181 helix: 2.32 (0.27), residues: 357 sheet: 0.71 (0.21), residues: 549 loop : -0.44 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 36 HIS 0.010 0.002 HIS I 26 PHE 0.035 0.003 PHE G 118 TYR 0.023 0.002 TYR D 162 ARG 0.009 0.001 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 208 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: B 171 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: C 144 LYS cc_start: 0.7862 (ptmm) cc_final: 0.7528 (mmmt) REVERT: D 72 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7425 (pttt) REVERT: H 61 GLN cc_start: 0.7342 (tp40) cc_final: 0.7122 (tp40) REVERT: H 100 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8298 (mt-10) REVERT: I 72 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7734 (ptmt) REVERT: J 80 MET cc_start: 0.7950 (tmm) cc_final: 0.7591 (tmm) outliers start: 69 outliers final: 39 residues processed: 247 average time/residue: 1.1735 time to fit residues: 327.5419 Evaluate side-chains 221 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 295 GLN Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 180 optimal weight: 0.0270 chunk 146 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS G 295 GLN I 26 HIS K 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17928 Z= 0.225 Angle : 0.551 11.648 24327 Z= 0.294 Chirality : 0.044 0.193 2652 Planarity : 0.004 0.043 3150 Dihedral : 5.658 77.495 2780 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.60 % Allowed : 13.09 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2181 helix: 2.36 (0.27), residues: 366 sheet: 0.72 (0.21), residues: 543 loop : -0.38 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.009 0.001 HIS I 26 PHE 0.022 0.002 PHE C 118 TYR 0.025 0.001 TYR B 162 ARG 0.009 0.001 ARG F 95A *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 171 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: C 144 LYS cc_start: 0.7803 (ptmm) cc_final: 0.7489 (mmmt) REVERT: G 285 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7393 (mm-40) REVERT: H 50 ARG cc_start: 0.8728 (ptt-90) cc_final: 0.8480 (ptt90) REVERT: H 100 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8269 (mt-10) REVERT: I 72 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7647 (ptmt) outliers start: 49 outliers final: 26 residues processed: 219 average time/residue: 1.2488 time to fit residues: 307.8733 Evaluate side-chains 203 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 29 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 0.0050 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS K 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17928 Z= 0.303 Angle : 0.578 11.301 24327 Z= 0.306 Chirality : 0.044 0.194 2652 Planarity : 0.005 0.041 3150 Dihedral : 5.542 75.303 2780 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.18 % Allowed : 13.35 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.18), residues: 2181 helix: 2.58 (0.27), residues: 357 sheet: 0.62 (0.21), residues: 573 loop : -0.39 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.009 0.001 HIS I 26 PHE 0.024 0.002 PHE C 118 TYR 0.023 0.002 TYR B 162 ARG 0.009 0.001 ARG F 95A *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7492 (mmmt) REVERT: D 131 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8518 (tttp) REVERT: G 285 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7315 (mm-40) REVERT: G 295 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: I 72 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7598 (ptmt) REVERT: J 80 MET cc_start: 0.8099 (tmm) cc_final: 0.7876 (tmm) outliers start: 60 outliers final: 39 residues processed: 222 average time/residue: 1.2095 time to fit residues: 302.4008 Evaluate side-chains 222 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 295 GLN Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 128 optimal weight: 0.0870 chunk 97 optimal weight: 9.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS K 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17928 Z= 0.234 Angle : 0.549 10.635 24327 Z= 0.291 Chirality : 0.043 0.207 2652 Planarity : 0.004 0.047 3150 Dihedral : 5.375 73.476 2780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.65 % Allowed : 13.78 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.18), residues: 2181 helix: 2.57 (0.27), residues: 360 sheet: 0.65 (0.21), residues: 603 loop : -0.40 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 92 HIS 0.009 0.001 HIS I 26 PHE 0.021 0.002 PHE C 118 TYR 0.024 0.001 TYR B 162 ARG 0.011 0.001 ARG F 95A *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7801 (ptmm) cc_final: 0.7499 (mmmt) REVERT: D 131 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8501 (tttp) REVERT: E 61 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7304 (tp40) REVERT: G 285 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7288 (mm-40) REVERT: G 295 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: H 50 ARG cc_start: 0.8737 (ptt90) cc_final: 0.8402 (ptt180) REVERT: H 100 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8194 (mt-10) REVERT: I 72 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7592 (ptmt) outliers start: 50 outliers final: 33 residues processed: 214 average time/residue: 1.2230 time to fit residues: 294.8961 Evaluate side-chains 215 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 295 GLN Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS K 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17928 Z= 0.230 Angle : 0.541 9.875 24327 Z= 0.287 Chirality : 0.043 0.186 2652 Planarity : 0.004 0.049 3150 Dihedral : 5.200 69.896 2780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 13.99 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2181 helix: 2.71 (0.27), residues: 363 sheet: 0.59 (0.20), residues: 609 loop : -0.34 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.010 0.001 HIS I 26 PHE 0.020 0.002 PHE I 110 TYR 0.025 0.001 TYR B 162 ARG 0.012 0.001 ARG K 95A *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7817 (ptmm) cc_final: 0.7501 (mmmt) REVERT: D 131 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8510 (tttp) REVERT: E 61 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7306 (tp40) REVERT: H 50 ARG cc_start: 0.8717 (ptt90) cc_final: 0.8384 (ptt180) REVERT: H 100 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8175 (mt-10) REVERT: I 72 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7588 (ptmt) outliers start: 49 outliers final: 31 residues processed: 228 average time/residue: 1.2122 time to fit residues: 310.8265 Evaluate side-chains 213 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS I 62 GLN K 29 ASN L 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 17928 Z= 0.572 Angle : 0.716 10.500 24327 Z= 0.372 Chirality : 0.050 0.223 2652 Planarity : 0.005 0.054 3150 Dihedral : 5.804 68.633 2778 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.91 % Allowed : 14.63 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2181 helix: 2.42 (0.28), residues: 357 sheet: 0.69 (0.22), residues: 531 loop : -0.62 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 127 HIS 0.008 0.002 HIS A 18 PHE 0.036 0.003 PHE A 118 TYR 0.027 0.003 TYR B 162 ARG 0.012 0.001 ARG K 95A *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7925 (ptmm) cc_final: 0.7512 (mmmt) REVERT: D 72 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7322 (pttt) REVERT: E 61 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7283 (tp40) REVERT: H 50 ARG cc_start: 0.8798 (ptt90) cc_final: 0.8395 (ptt180) REVERT: H 100 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8296 (mt-10) REVERT: J 80 MET cc_start: 0.8198 (tmm) cc_final: 0.7984 (tmm) outliers start: 55 outliers final: 41 residues processed: 231 average time/residue: 1.1777 time to fit residues: 307.9126 Evaluate side-chains 225 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17928 Z= 0.232 Angle : 0.569 9.191 24327 Z= 0.301 Chirality : 0.043 0.240 2652 Planarity : 0.005 0.077 3150 Dihedral : 5.399 66.250 2778 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.23 % Allowed : 16.11 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.18), residues: 2181 helix: 2.68 (0.28), residues: 357 sheet: 0.65 (0.21), residues: 591 loop : -0.54 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 14 HIS 0.010 0.001 HIS I 26 PHE 0.021 0.002 PHE A 294 TYR 0.024 0.001 TYR B 162 ARG 0.017 0.001 ARG L 95A ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7802 (ptmm) cc_final: 0.7513 (mmmt) REVERT: D 72 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7390 (pttt) REVERT: E 61 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7250 (tp40) REVERT: H 50 ARG cc_start: 0.8739 (ptt90) cc_final: 0.8291 (ptt180) REVERT: H 100 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8402 (mt-10) REVERT: I 72 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7695 (ptmt) outliers start: 42 outliers final: 30 residues processed: 218 average time/residue: 1.1938 time to fit residues: 294.3947 Evaluate side-chains 209 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 0.0060 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.184052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147686 restraints weight = 20325.937| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.43 r_work: 0.3461 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17928 Z= 0.203 Angle : 0.546 8.424 24327 Z= 0.288 Chirality : 0.043 0.212 2652 Planarity : 0.005 0.084 3150 Dihedral : 5.064 62.558 2778 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.12 % Allowed : 16.22 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.18), residues: 2181 helix: 2.74 (0.28), residues: 363 sheet: 0.72 (0.21), residues: 591 loop : -0.45 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 14 HIS 0.010 0.001 HIS I 26 PHE 0.021 0.002 PHE J 63 TYR 0.023 0.001 TYR B 162 ARG 0.019 0.001 ARG L 95A Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6055.13 seconds wall clock time: 106 minutes 55.58 seconds (6415.58 seconds total)