Starting phenix.real_space_refine on Sun May 18 19:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp5_41467/05_2025/8tp5_41467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp5_41467/05_2025/8tp5_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/cci-nas-00/data/ceres_data/8tp5_41467/05_2025/8tp5_41467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp5_41467/05_2025/8tp5_41467.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp5_41467/05_2025/8tp5_41467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp5_41467/05_2025/8tp5_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. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.89, per 1000 atoms: 0.56 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 - 3.00 Amino acid : True - 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: 4.68 Conformation dependent library (CDL) restraints added in 2.3 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: 3.07 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: 5.48 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: 0.00 - 7.35: 24283 7.35 - 14.71: 32 14.71 - 22.06: 0 22.06 - 29.41: 0 29.41 - 36.77: 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: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.180 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.330 ------------------------------------------------------------------------------- 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 17970 Z= 1.108 Angle : 1.864 36.768 24429 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 Details of bonding type rmsd link_NAG-ASN : bond 0.07961 ( 15) link_NAG-ASN : angle 3.21227 ( 45) link_BETA1-4 : bond 0.07581 ( 3) link_BETA1-4 : angle 4.35365 ( 9) hydrogen bonds : bond 0.15716 ( 722) hydrogen bonds : angle 7.73041 ( 2043) SS BOND : bond 0.02370 ( 24) SS BOND : angle 2.30850 ( 48) covalent geometry : bond 0.02096 (17928) covalent geometry : angle 1.85815 (24327) *********************** 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 to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 1.875 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: 1.3003 time to fit residues: 551.3378 Evaluate side-chains 186 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.182344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133563 restraints weight = 20634.923| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.58 r_work: 0.3330 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 17970 Z= 0.164 Angle : 0.616 6.843 24429 Z= 0.334 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 15) link_NAG-ASN : angle 2.59587 ( 45) link_BETA1-4 : bond 0.00235 ( 3) link_BETA1-4 : angle 1.27446 ( 9) hydrogen bonds : bond 0.05482 ( 722) hydrogen bonds : angle 5.88257 ( 2043) SS BOND : bond 0.00253 ( 24) SS BOND : angle 0.90504 ( 48) covalent geometry : bond 0.00350 (17928) covalent geometry : angle 0.60505 (24327) *********************** 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 to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7383 (p0) cc_final: 0.6758 (p0) REVERT: B 77 MET cc_start: 0.8259 (mmm) cc_final: 0.8031 (mtp) REVERT: C 75 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: C 144 LYS cc_start: 0.7796 (ptmm) cc_final: 0.7130 (mmmt) REVERT: C 238 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8269 (mm-30) REVERT: C 285 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: C 323 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8352 (pt) REVERT: D 124 SER cc_start: 0.8895 (m) cc_final: 0.8675 (p) REVERT: E 56 MET cc_start: 0.8341 (mtp) cc_final: 0.7946 (ptp) REVERT: G 21 ASN cc_start: 0.7800 (p0) cc_final: 0.7500 (p0) REVERT: G 32 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7654 (tppt) REVERT: G 45 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7467 (p0) REVERT: G 144 LYS cc_start: 0.7602 (ptmm) cc_final: 0.7035 (mmmt) REVERT: G 285 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7452 (mm-40) REVERT: I 43 ASN cc_start: 0.8357 (t0) cc_final: 0.8022 (m-40) REVERT: I 72 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7640 (ptmt) REVERT: I 123 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8259 (ttmt) REVERT: J 89 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7551 (tpt) REVERT: K 29 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7977 (m-40) outliers start: 56 outliers final: 23 residues processed: 235 average time/residue: 1.1705 time to fit residues: 309.9734 Evaluate side-chains 194 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 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 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 45 ASP 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 89 MET 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 59 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 203 optimal weight: 0.0670 chunk 172 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 295 GLN B 26 HIS D 26 HIS G 190 ASN G 199 ASN G 295 GLN I 26 HIS K 29 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 160)---------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134023 restraints weight = 20235.345| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.53 r_work: 0.3413 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17970 Z= 0.155 Angle : 0.559 6.938 24429 Z= 0.302 Chirality : 0.045 0.223 2652 Planarity : 0.004 0.037 3150 Dihedral : 5.930 82.014 2780 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.07 % Allowed : 9.80 % Favored : 87.12 % 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: 0.92 (0.17), residues: 2181 helix: 2.33 (0.26), residues: 360 sheet: 0.82 (0.21), residues: 564 loop : 0.06 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 36 HIS 0.010 0.002 HIS I 26 PHE 0.030 0.002 PHE A 118 TYR 0.013 0.001 TYR D 162 ARG 0.006 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 15) link_NAG-ASN : angle 2.02567 ( 45) link_BETA1-4 : bond 0.00246 ( 3) link_BETA1-4 : angle 1.27713 ( 9) hydrogen bonds : bond 0.04883 ( 722) hydrogen bonds : angle 5.39316 ( 2043) SS BOND : bond 0.00390 ( 24) SS BOND : angle 1.36905 ( 48) covalent geometry : bond 0.00352 (17928) covalent geometry : angle 0.54954 (24327) *********************** 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 259 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: B 24 TYR cc_start: 0.8911 (m-80) cc_final: 0.8602 (m-80) REVERT: B 77 MET cc_start: 0.8256 (mmm) cc_final: 0.8016 (mtp) REVERT: B 113 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8341 (m) REVERT: C 144 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7295 (mmmt) REVERT: C 238 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8095 (mm-30) REVERT: C 246 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7273 (mt-10) REVERT: C 285 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7988 (mm-40) REVERT: D 124 SER cc_start: 0.8899 (m) cc_final: 0.8685 (p) REVERT: G 21 ASN cc_start: 0.7721 (p0) cc_final: 0.7477 (p0) REVERT: G 32 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7637 (tppt) REVERT: G 144 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7247 (mmmt) REVERT: H 61 GLN cc_start: 0.7691 (tp40) cc_final: 0.7473 (tp40) REVERT: I 72 LYS cc_start: 0.8186 (pttm) cc_final: 0.7680 (ptmt) REVERT: I 123 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8307 (ttmt) REVERT: K 29 ASN cc_start: 0.8349 (m110) cc_final: 0.7916 (m-40) outliers start: 58 outliers final: 22 residues processed: 234 average time/residue: 1.1858 time to fit residues: 312.5299 Evaluate side-chains 200 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 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 131 LYS 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 G residue 295 GLN Chi-restraints excluded: chain H residue 21 SER 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 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 89 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 197 optimal weight: 0.0770 chunk 169 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 190 ASN A 295 GLN B 26 HIS C 141 HIS D 26 HIS D 60 ASN G 199 ASN G 295 GLN I 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.179209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137808 restraints weight = 20165.597| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.57 r_work: 0.3287 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17970 Z= 0.167 Angle : 0.579 11.809 24429 Z= 0.307 Chirality : 0.044 0.219 2652 Planarity : 0.004 0.039 3150 Dihedral : 5.605 80.043 2780 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.86 % Allowed : 11.08 % Favored : 86.06 % 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: 0.82 (0.17), residues: 2181 helix: 2.42 (0.27), residues: 360 sheet: 0.81 (0.21), residues: 564 loop : -0.10 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 36 HIS 0.009 0.001 HIS I 26 PHE 0.027 0.002 PHE G 118 TYR 0.022 0.001 TYR D 162 ARG 0.009 0.001 ARG F 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 15) link_NAG-ASN : angle 1.94360 ( 45) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.27613 ( 9) hydrogen bonds : bond 0.04750 ( 722) hydrogen bonds : angle 5.29521 ( 2043) SS BOND : bond 0.00369 ( 24) SS BOND : angle 2.05554 ( 48) covalent geometry : bond 0.00392 (17928) covalent geometry : angle 0.56640 (24327) *********************** 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 249 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7801 (pp30) REVERT: B 113 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8589 (m) REVERT: B 171 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: C 21 ASN cc_start: 0.7628 (p0) cc_final: 0.7364 (p0) REVERT: C 144 LYS cc_start: 0.7885 (ptmm) cc_final: 0.7416 (mmmt) REVERT: C 246 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 285 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8125 (mm-40) REVERT: G 32 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7707 (tppt) REVERT: G 144 LYS cc_start: 0.7790 (ptmm) cc_final: 0.7384 (mmmt) REVERT: G 295 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: H 61 GLN cc_start: 0.7638 (tp40) cc_final: 0.7384 (tp40) REVERT: I 72 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7694 (ptmt) outliers start: 54 outliers final: 30 residues processed: 224 average time/residue: 1.1426 time to fit residues: 289.5600 Evaluate side-chains 209 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 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 113 SER 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 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 113 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 110 THR 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 G residue 78 LEU Chi-restraints excluded: chain G residue 295 GLN 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 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 178 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 156 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 295 GLN B 26 HIS D 26 HIS G 295 GLN I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.180801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134169 restraints weight = 20480.086| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.66 r_work: 0.3383 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17970 Z= 0.121 Angle : 0.525 13.229 24429 Z= 0.279 Chirality : 0.042 0.190 2652 Planarity : 0.004 0.042 3150 Dihedral : 5.308 78.157 2778 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.54 % Allowed : 12.29 % Favored : 85.16 % 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: 0.88 (0.18), residues: 2181 helix: 2.67 (0.26), residues: 357 sheet: 0.83 (0.21), residues: 564 loop : -0.12 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.009 0.001 HIS D 26 PHE 0.020 0.001 PHE A 118 TYR 0.025 0.001 TYR B 162 ARG 0.008 0.000 ARG F 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 15) link_NAG-ASN : angle 1.66667 ( 45) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 1.17934 ( 9) hydrogen bonds : bond 0.04327 ( 722) hydrogen bonds : angle 5.12347 ( 2043) SS BOND : bond 0.00485 ( 24) SS BOND : angle 1.59770 ( 48) covalent geometry : bond 0.00274 (17928) covalent geometry : angle 0.51560 (24327) *********************** 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 238 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7323 (pp30) REVERT: B 113 SER cc_start: 0.8776 (p) cc_final: 0.8482 (m) REVERT: B 171 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6200 (pm20) REVERT: C 21 ASN cc_start: 0.7636 (p0) cc_final: 0.7339 (p0) REVERT: C 144 LYS cc_start: 0.7849 (ptmm) cc_final: 0.7281 (mmmt) REVERT: C 246 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 285 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: D 116 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8054 (ttmm) REVERT: D 131 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8330 (tttp) REVERT: G 32 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7689 (tppt) REVERT: G 144 LYS cc_start: 0.7814 (ptmm) cc_final: 0.7297 (mmmt) REVERT: G 295 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7671 (pp30) REVERT: H 61 GLN cc_start: 0.7727 (tp40) cc_final: 0.7517 (tp40) REVERT: H 100 PHE cc_start: 0.8554 (m-80) cc_final: 0.8273 (m-80) REVERT: I 72 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7675 (ptmt) REVERT: J 89 MET cc_start: 0.8135 (tpt) cc_final: 0.7828 (tpt) REVERT: K 29 ASN cc_start: 0.8431 (m110) cc_final: 0.8042 (m-40) outliers start: 48 outliers final: 21 residues processed: 223 average time/residue: 1.0438 time to fit residues: 265.4118 Evaluate side-chains 199 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 171 GLU Chi-restraints excluded: chain C residue 78 LEU 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 113 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 137 CYS 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 93 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 295 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 110 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 135 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 141 HIS G 295 GLN I 26 HIS L 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.178470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 172)---------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130190 restraints weight = 20376.548| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.48 r_work: 0.3381 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17970 Z= 0.157 Angle : 0.550 11.339 24429 Z= 0.290 Chirality : 0.043 0.165 2652 Planarity : 0.004 0.040 3150 Dihedral : 5.276 75.785 2778 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 12.35 % Favored : 84.90 % 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: 0.83 (0.18), residues: 2181 helix: 2.64 (0.27), residues: 363 sheet: 0.80 (0.21), residues: 564 loop : -0.17 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 36 HIS 0.010 0.001 HIS D 26 PHE 0.024 0.002 PHE A 118 TYR 0.024 0.001 TYR B 162 ARG 0.010 0.001 ARG K 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 15) link_NAG-ASN : angle 1.81600 ( 45) link_BETA1-4 : bond 0.00203 ( 3) link_BETA1-4 : angle 1.23188 ( 9) hydrogen bonds : bond 0.04434 ( 722) hydrogen bonds : angle 5.13024 ( 2043) SS BOND : bond 0.00547 ( 24) SS BOND : angle 1.46683 ( 48) covalent geometry : bond 0.00374 (17928) covalent geometry : angle 0.54151 (24327) *********************** 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 242 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7485 (pp30) REVERT: B 113 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8441 (m) REVERT: B 116 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8168 (ttmm) REVERT: B 171 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: C 21 ASN cc_start: 0.7619 (p0) cc_final: 0.7337 (p0) REVERT: C 144 LYS cc_start: 0.7866 (ptmm) cc_final: 0.7289 (mmmt) REVERT: C 246 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7533 (mt-10) REVERT: C 285 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8068 (mm-40) REVERT: D 106 ARG cc_start: 0.7659 (mmp80) cc_final: 0.7426 (mmp80) REVERT: D 116 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7976 (ttmm) REVERT: D 131 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8360 (tttp) REVERT: F 29 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7093 (m110) REVERT: G 144 LYS cc_start: 0.7734 (ptmm) cc_final: 0.7241 (mmmt) REVERT: G 285 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7720 (mm-40) REVERT: I 72 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7665 (ptmt) REVERT: I 116 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7751 (ttmm) REVERT: J 89 MET cc_start: 0.8314 (tpt) cc_final: 0.7942 (tpt) REVERT: K 29 ASN cc_start: 0.8516 (m110) cc_final: 0.8146 (m-40) outliers start: 52 outliers final: 32 residues processed: 220 average time/residue: 1.1217 time to fit residues: 279.8616 Evaluate side-chains 217 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 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 113 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 285 GLN 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 D residue 137 CYS 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 G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 295 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 J residue 21 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 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 93 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 59 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 L 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128514 restraints weight = 20344.335| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.52 r_work: 0.3305 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17970 Z= 0.233 Angle : 0.624 10.357 24429 Z= 0.324 Chirality : 0.046 0.156 2652 Planarity : 0.005 0.041 3150 Dihedral : 5.497 73.155 2778 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.18 % Allowed : 12.82 % Favored : 84.00 % 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: 0.67 (0.18), residues: 2181 helix: 2.61 (0.27), residues: 357 sheet: 0.64 (0.21), residues: 579 loop : -0.27 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.010 0.002 HIS I 26 PHE 0.031 0.002 PHE C 118 TYR 0.025 0.002 TYR B 162 ARG 0.006 0.001 ARG K 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 15) link_NAG-ASN : angle 2.09994 ( 45) link_BETA1-4 : bond 0.00120 ( 3) link_BETA1-4 : angle 1.47228 ( 9) hydrogen bonds : bond 0.04815 ( 722) hydrogen bonds : angle 5.28336 ( 2043) SS BOND : bond 0.00596 ( 24) SS BOND : angle 1.58641 ( 48) covalent geometry : bond 0.00566 (17928) covalent geometry : angle 0.61383 (24327) *********************** 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 250 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (m) REVERT: B 116 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8220 (ttmm) REVERT: C 21 ASN cc_start: 0.7815 (p0) cc_final: 0.7501 (p0) REVERT: C 144 LYS cc_start: 0.7926 (ptmm) cc_final: 0.7272 (mmmt) REVERT: C 246 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7654 (mt-10) REVERT: D 72 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7579 (pttt) REVERT: D 116 LYS cc_start: 0.8334 (mtpp) cc_final: 0.8015 (ttmm) REVERT: D 131 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8295 (tttp) REVERT: E 100 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8716 (mt-10) REVERT: G 144 LYS cc_start: 0.7787 (ptmm) cc_final: 0.7286 (mmmt) REVERT: G 285 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7885 (mm-40) REVERT: G 295 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: G 310 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7851 (ptp90) REVERT: H 100 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8573 (mt-10) REVERT: I 72 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7769 (ptmt) REVERT: I 116 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7830 (ttmm) REVERT: J 63 PHE cc_start: 0.8045 (m-80) cc_final: 0.7596 (m-80) outliers start: 60 outliers final: 36 residues processed: 223 average time/residue: 1.2007 time to fit residues: 301.2813 Evaluate side-chains 223 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP 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 113 SER 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 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 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 J residue 21 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 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 47 LEU 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 167 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS G 295 GLN I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127348 restraints weight = 20223.408| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.88 r_work: 0.3343 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17970 Z= 0.132 Angle : 0.546 9.396 24429 Z= 0.288 Chirality : 0.043 0.151 2652 Planarity : 0.004 0.081 3150 Dihedral : 5.241 70.995 2778 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.44 % Allowed : 13.46 % Favored : 84.10 % 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: 0.74 (0.18), residues: 2181 helix: 2.68 (0.27), residues: 363 sheet: 0.64 (0.21), residues: 579 loop : -0.21 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.010 0.001 HIS I 26 PHE 0.021 0.002 PHE C 118 TYR 0.025 0.001 TYR B 162 ARG 0.018 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 15) link_NAG-ASN : angle 1.72651 ( 45) link_BETA1-4 : bond 0.00295 ( 3) link_BETA1-4 : angle 1.31303 ( 9) hydrogen bonds : bond 0.04274 ( 722) hydrogen bonds : angle 5.12950 ( 2043) SS BOND : bond 0.00522 ( 24) SS BOND : angle 1.56092 ( 48) covalent geometry : bond 0.00307 (17928) covalent geometry : angle 0.53752 (24327) *********************** 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 235 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.8052 (tt0) cc_final: 0.7639 (tp30) REVERT: B 113 SER cc_start: 0.8711 (p) cc_final: 0.8394 (m) REVERT: B 116 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8013 (ttmm) REVERT: C 144 LYS cc_start: 0.7866 (ptmm) cc_final: 0.7193 (mmmt) REVERT: C 246 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7588 (mt-10) REVERT: D 106 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7701 (mtp-110) REVERT: D 116 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7828 (ttmm) REVERT: D 131 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8202 (tttp) REVERT: E 100 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8635 (mt-10) REVERT: F 29 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.6818 (m110) REVERT: G 60 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: G 144 LYS cc_start: 0.7767 (ptmm) cc_final: 0.7195 (mmmt) REVERT: G 285 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7715 (mm-40) REVERT: G 295 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7865 (pp30) REVERT: G 310 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7822 (ptp90) REVERT: H 100 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8603 (mt-10) REVERT: I 72 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7688 (ptmt) REVERT: I 116 LYS cc_start: 0.8104 (mtpm) cc_final: 0.7648 (ttmm) REVERT: J 63 PHE cc_start: 0.8014 (m-80) cc_final: 0.7562 (m-80) REVERT: J 89 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8062 (tpt) REVERT: K 29 ASN cc_start: 0.8700 (m110) cc_final: 0.8258 (m-40) outliers start: 46 outliers final: 30 residues processed: 214 average time/residue: 1.1583 time to fit residues: 282.7333 Evaluate side-chains 214 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 171 GLU 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 60 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 SER 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 89 LEU 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 89 MET 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 135 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 L 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129838 restraints weight = 20391.779| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.63 r_work: 0.3099 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17970 Z= 0.253 Angle : 0.654 9.456 24429 Z= 0.339 Chirality : 0.046 0.153 2652 Planarity : 0.005 0.069 3150 Dihedral : 5.519 69.543 2778 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.86 % Allowed : 13.88 % Favored : 83.25 % 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: 2.63 (0.27), residues: 357 sheet: 0.68 (0.22), residues: 549 loop : -0.38 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 36 HIS 0.008 0.002 HIS D 26 PHE 0.031 0.002 PHE C 118 TYR 0.026 0.002 TYR B 162 ARG 0.018 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 15) link_NAG-ASN : angle 2.22588 ( 45) link_BETA1-4 : bond 0.00239 ( 3) link_BETA1-4 : angle 1.55377 ( 9) hydrogen bonds : bond 0.04910 ( 722) hydrogen bonds : angle 5.32929 ( 2043) SS BOND : bond 0.00607 ( 24) SS BOND : angle 1.60537 ( 48) covalent geometry : bond 0.00619 (17928) covalent geometry : angle 0.64346 (24327) *********************** 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 251 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.8058 (tt0) cc_final: 0.7522 (tp30) REVERT: B 113 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8340 (m) REVERT: C 144 LYS cc_start: 0.7860 (ptmm) cc_final: 0.7020 (mmmt) REVERT: C 246 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7782 (mt-10) REVERT: D 72 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7525 (pttt) REVERT: D 106 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7566 (mtp-110) REVERT: D 116 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7784 (ttmm) REVERT: D 131 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8207 (tttp) REVERT: G 60 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: G 144 LYS cc_start: 0.7719 (ptmm) cc_final: 0.7023 (mmmt) REVERT: G 285 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7910 (mm-40) REVERT: G 295 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: I 116 LYS cc_start: 0.8168 (mtpm) cc_final: 0.7682 (ttmm) REVERT: J 63 PHE cc_start: 0.7945 (m-80) cc_final: 0.7450 (m-80) REVERT: J 89 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7975 (tpt) REVERT: K 29 ASN cc_start: 0.8888 (m110) cc_final: 0.8461 (m-40) outliers start: 54 outliers final: 38 residues processed: 226 average time/residue: 1.2196 time to fit residues: 309.4983 Evaluate side-chains 233 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 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 113 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 171 GLU 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 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 60 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 SER 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 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 89 MET 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 47 LEU 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 137 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 chunk 101 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 G 295 GLN I 26 HIS I 60 ASN L 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129933 restraints weight = 20297.134| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.62 r_work: 0.3158 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17970 Z= 0.127 Angle : 0.543 8.444 24429 Z= 0.286 Chirality : 0.042 0.150 2652 Planarity : 0.005 0.083 3150 Dihedral : 5.153 66.938 2778 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.23 % Allowed : 14.89 % Favored : 82.88 % 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: 0.67 (0.18), residues: 2181 helix: 2.70 (0.27), residues: 363 sheet: 0.62 (0.21), residues: 609 loop : -0.33 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 127 HIS 0.010 0.001 HIS D 26 PHE 0.025 0.002 PHE A 294 TYR 0.024 0.001 TYR B 162 ARG 0.019 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.68019 ( 45) link_BETA1-4 : bond 0.00390 ( 3) link_BETA1-4 : angle 1.38497 ( 9) hydrogen bonds : bond 0.04198 ( 722) hydrogen bonds : angle 5.14755 ( 2043) SS BOND : bond 0.00465 ( 24) SS BOND : angle 1.33485 ( 48) covalent geometry : bond 0.00292 (17928) covalent geometry : angle 0.53529 (24327) ********************** 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 238 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7635 (pp30) cc_final: 0.7413 (pm20) REVERT: B 105 GLU cc_start: 0.7871 (tt0) cc_final: 0.7315 (tp30) REVERT: B 113 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8171 (m) REVERT: B 116 LYS cc_start: 0.8165 (mtpm) cc_final: 0.7621 (ttmm) REVERT: C 144 LYS cc_start: 0.7723 (ptmm) cc_final: 0.6893 (mmmt) REVERT: C 149 ARG cc_start: 0.8465 (mtm180) cc_final: 0.8163 (mtp180) REVERT: C 246 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 106 ARG cc_start: 0.7797 (mmp80) cc_final: 0.7445 (mtp-110) REVERT: D 116 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7652 (ttmm) REVERT: D 131 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8177 (tttp) REVERT: E 61 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7659 (tp40) REVERT: F 29 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6753 (p0) REVERT: G 60 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: G 144 LYS cc_start: 0.7670 (ptmm) cc_final: 0.6944 (mmmt) REVERT: G 285 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7655 (mm-40) REVERT: H 50 ARG cc_start: 0.8535 (ptt90) cc_final: 0.7974 (ptt180) REVERT: H 100 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8529 (mp0) REVERT: I 72 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7705 (ptmt) REVERT: J 63 PHE cc_start: 0.7931 (m-80) cc_final: 0.7395 (m-80) REVERT: J 89 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7903 (tpt) REVERT: K 29 ASN cc_start: 0.8717 (m110) cc_final: 0.8390 (m110) outliers start: 42 outliers final: 29 residues processed: 219 average time/residue: 1.1892 time to fit residues: 293.1673 Evaluate side-chains 214 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain B residue 171 GLU 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 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 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 60 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 SER 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 H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS 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 89 MET Chi-restraints excluded: chain J residue 110 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 119 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 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 295 GLN B 26 HIS D 26 HIS G 295 GLN I 26 HIS L 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130318 restraints weight = 20219.671| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.63 r_work: 0.3147 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17970 Z= 0.149 Angle : 0.551 8.096 24429 Z= 0.289 Chirality : 0.043 0.151 2652 Planarity : 0.004 0.056 3150 Dihedral : 5.044 64.148 2778 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.54 % Allowed : 15.10 % Favored : 82.35 % 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: 0.70 (0.18), residues: 2181 helix: 2.76 (0.27), residues: 363 sheet: 0.65 (0.21), residues: 609 loop : -0.33 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 36 HIS 0.010 0.001 HIS I 26 PHE 0.022 0.002 PHE C 118 TYR 0.022 0.001 TYR B 162 ARG 0.012 0.001 ARG K 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 15) link_NAG-ASN : angle 1.78375 ( 45) link_BETA1-4 : bond 0.00193 ( 3) link_BETA1-4 : angle 1.29034 ( 9) hydrogen bonds : bond 0.04237 ( 722) hydrogen bonds : angle 5.12758 ( 2043) SS BOND : bond 0.00482 ( 24) SS BOND : angle 1.26266 ( 48) covalent geometry : bond 0.00355 (17928) covalent geometry : angle 0.54362 (24327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14020.09 seconds wall clock time: 241 minutes 48.04 seconds (14508.04 seconds total)