Starting phenix.real_space_refine on Sun Jun 15 13:56:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp5_41467/06_2025/8tp5_41467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp5_41467/06_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_41467/06_2025/8tp5_41467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp5_41467/06_2025/8tp5_41467.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp5_41467/06_2025/8tp5_41467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp5_41467/06_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-5710/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: 11.15, per 1000 atoms: 0.64 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: 4.91 Conformation dependent library (CDL) restraints added in 2.2 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 51 sheets defined 21.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 29 through 30C Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP G 127 " --> pdb=" O LYS G 125A" (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.749A pdb=" N LEU A 51 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA A 279 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A 53 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 144 through 146 removed outlier: 9.996A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.749A pdb=" N LEU C 51 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 53 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 144 through 146 removed outlier: 9.995A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER F 2 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 98 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS F 88 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER F 2 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 98 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS F 88 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 18 through 24 Processing sheet with id=AD2, first strand: chain 'I' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS I 137 " --> pdb=" O ILE I 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'G' and resid 51 through 54 removed outlier: 7.748A pdb=" N LEU G 51 " --> pdb=" O CYS G 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA G 279 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 53 " --> pdb=" O ALA G 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 144 through 146 removed outlier: 9.995A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE3, first strand: chain 'G' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'K' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER K 2 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 98 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER K 2 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 98 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF4, first strand: chain 'L' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER L 2 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE L 98 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER L 2 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE L 98 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 24 788 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 5.76 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: 0.12 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: 14.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.430 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.770 ------------------------------------------------------------------------------- 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 : 1.916 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: 1.3607 time to fit residues: 577.6308 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 : 1.939 ------------------------------------------------------------------------------- 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 = 101)---------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128703 restraints weight = 20634.924| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.96 r_work: 0.3331 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7467 (p0) cc_final: 0.6842 (p0) REVERT: B 77 MET cc_start: 0.8335 (mmm) cc_final: 0.8130 (mtp) REVERT: C 75 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: C 144 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7258 (mmmt) REVERT: C 285 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: C 323 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8398 (pt) REVERT: D 124 SER cc_start: 0.8906 (m) cc_final: 0.8705 (p) REVERT: E 56 MET cc_start: 0.8365 (mtp) cc_final: 0.7984 (ptp) REVERT: G 21 ASN cc_start: 0.7857 (p0) cc_final: 0.7558 (p0) REVERT: G 32 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7721 (tppt) REVERT: G 45 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7535 (p0) REVERT: G 144 LYS cc_start: 0.7692 (ptmm) cc_final: 0.7177 (mmmt) REVERT: G 285 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7617 (mm-40) REVERT: I 43 ASN cc_start: 0.8381 (t0) cc_final: 0.8065 (m-40) REVERT: I 72 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7661 (ptmt) REVERT: I 123 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8358 (ttmt) REVERT: J 89 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7666 (tpt) REVERT: K 29 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8090 (m-40) outliers start: 56 outliers final: 23 residues processed: 235 average time/residue: 1.2631 time to fit residues: 334.6295 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 : 1.826 ------------------------------------------------------------------------------- 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: 6.9990 chunk 203 optimal weight: 0.0470 chunk 172 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 190 ASN G 199 ASN G 295 GLN I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135270 restraints weight = 20241.799| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.56 r_work: 0.3365 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3304 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= 0.150 Angle : 0.556 7.033 24429 Z= 0.301 Chirality : 0.044 0.209 2652 Planarity : 0.004 0.037 3150 Dihedral : 5.920 82.022 2780 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.07 % Allowed : 9.70 % Favored : 87.23 % 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: 0.91 (0.17), residues: 2181 helix: 2.33 (0.26), residues: 360 sheet: 0.81 (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 0.031 0.002 PHE A 118 TYR 0.016 0.001 TYR B 162 ARG 0.012 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 15) link_NAG-ASN : angle 1.97456 ( 45) link_BETA1-4 : bond 0.00170 ( 3) link_BETA1-4 : angle 1.29802 ( 9) hydrogen bonds : bond 0.04880 ( 722) hydrogen bonds : angle 5.39490 ( 2043) SS BOND : bond 0.00435 ( 24) SS BOND : angle 1.07286 ( 48) covalent geometry : bond 0.00342 (17928) covalent geometry : angle 0.54764 (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 260 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7416 (pp30) REVERT: B 77 MET cc_start: 0.8287 (mmm) cc_final: 0.8060 (mtp) REVERT: B 113 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8276 (m) REVERT: C 144 LYS cc_start: 0.7836 (ptmm) cc_final: 0.7208 (mmmt) REVERT: C 246 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7274 (mt-10) REVERT: C 285 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7959 (mm-40) REVERT: D 124 SER cc_start: 0.8876 (m) cc_final: 0.8650 (p) REVERT: G 21 ASN cc_start: 0.7702 (p0) cc_final: 0.7444 (p0) REVERT: G 32 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7604 (tppt) REVERT: G 144 LYS cc_start: 0.7709 (ptmm) cc_final: 0.7150 (mmmt) REVERT: H 61 GLN cc_start: 0.7726 (tp40) cc_final: 0.7520 (tp40) REVERT: I 72 LYS cc_start: 0.8233 (pttm) cc_final: 0.7663 (ptmt) REVERT: I 77 MET cc_start: 0.8215 (ttp) cc_final: 0.7839 (mmm) REVERT: I 123 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8299 (ttmt) REVERT: K 29 ASN cc_start: 0.8262 (m110) cc_final: 0.7951 (m-40) outliers start: 58 outliers final: 23 residues processed: 234 average time/residue: 1.3281 time to fit residues: 351.7561 Evaluate side-chains 205 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 40 SER 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: 0.9990 chunk 169 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 194 optimal weight: 0.0060 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 L 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.180138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 157)---------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132395 restraints weight = 20116.234| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.57 r_work: 0.3391 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17970 Z= 0.158 Angle : 0.563 8.765 24429 Z= 0.299 Chirality : 0.044 0.229 2652 Planarity : 0.004 0.039 3150 Dihedral : 5.578 79.982 2780 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.86 % Allowed : 10.92 % Favored : 86.22 % 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: 0.84 (0.17), residues: 2181 helix: 2.43 (0.26), residues: 360 sheet: 0.81 (0.21), residues: 564 loop : -0.07 (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 A 118 TYR 0.022 0.001 TYR D 162 ARG 0.008 0.001 ARG F 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 15) link_NAG-ASN : angle 1.90658 ( 45) link_BETA1-4 : bond 0.00166 ( 3) link_BETA1-4 : angle 1.18307 ( 9) hydrogen bonds : bond 0.04694 ( 722) hydrogen bonds : angle 5.25401 ( 2043) SS BOND : bond 0.00394 ( 24) SS BOND : angle 1.77810 ( 48) covalent geometry : bond 0.00370 (17928) covalent geometry : angle 0.55160 (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 248 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 113 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8481 (m) REVERT: B 171 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: C 144 LYS cc_start: 0.7855 (ptmm) cc_final: 0.7296 (mmmt) REVERT: C 246 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 285 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: D 106 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7659 (mmp80) REVERT: D 131 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8376 (tttp) REVERT: G 21 ASN cc_start: 0.7849 (p0) cc_final: 0.7565 (p0) REVERT: G 32 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7648 (tppt) REVERT: G 144 LYS cc_start: 0.7732 (ptmm) cc_final: 0.7251 (mmmt) REVERT: G 295 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: H 61 GLN cc_start: 0.7753 (tp40) cc_final: 0.7520 (tp40) REVERT: I 72 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7678 (ptmt) REVERT: K 29 ASN cc_start: 0.8463 (m110) cc_final: 0.8262 (m-40) outliers start: 54 outliers final: 28 residues processed: 223 average time/residue: 1.2256 time to fit residues: 309.0258 Evaluate side-chains 207 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 152 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 141 HIS G 295 GLN I 26 HIS K 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.180130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134070 restraints weight = 20441.945| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.70 r_work: 0.3196 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17970 Z= 0.138 Angle : 0.536 9.479 24429 Z= 0.284 Chirality : 0.043 0.178 2652 Planarity : 0.004 0.041 3150 Dihedral : 5.317 77.717 2778 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.02 % Allowed : 11.45 % Favored : 85.53 % 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: 0.87 (0.18), residues: 2181 helix: 2.69 (0.26), residues: 357 sheet: 0.82 (0.21), residues: 564 loop : -0.13 (0.17), residues: 1260 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 0.021 0.002 PHE A 118 TYR 0.024 0.001 TYR B 162 ARG 0.008 0.000 ARG F 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 15) link_NAG-ASN : angle 1.74704 ( 45) link_BETA1-4 : bond 0.00139 ( 3) link_BETA1-4 : angle 1.19361 ( 9) hydrogen bonds : bond 0.04398 ( 722) hydrogen bonds : angle 5.11222 ( 2043) SS BOND : bond 0.00589 ( 24) SS BOND : angle 1.73610 ( 48) covalent geometry : bond 0.00319 (17928) covalent geometry : angle 0.52541 (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 261 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: B 113 SER cc_start: 0.8568 (p) cc_final: 0.8217 (m) REVERT: B 116 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7952 (ttmm) REVERT: C 21 ASN cc_start: 0.7594 (p0) cc_final: 0.7242 (p0) REVERT: C 144 LYS cc_start: 0.7762 (ptmm) cc_final: 0.6963 (mmmt) REVERT: C 246 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7497 (mt-10) REVERT: C 285 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: D 103 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7683 (mt-10) REVERT: D 106 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7339 (mmp80) REVERT: D 116 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7718 (ttmm) REVERT: G 32 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7585 (tppt) REVERT: G 144 LYS cc_start: 0.7681 (ptmm) cc_final: 0.6938 (mmmt) REVERT: G 285 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7684 (mm-40) REVERT: G 295 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: H 100 PHE cc_start: 0.8412 (m-80) cc_final: 0.8111 (m-80) REVERT: I 72 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7651 (ptmt) REVERT: I 116 LYS cc_start: 0.8015 (mtpm) cc_final: 0.7451 (ttmm) REVERT: J 91 TYR cc_start: 0.8498 (m-80) cc_final: 0.8283 (m-80) outliers start: 57 outliers final: 29 residues processed: 236 average time/residue: 1.3533 time to fit residues: 364.3526 Evaluate side-chains 212 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 307 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain 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 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 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 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 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 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: 0.9990 chunk 67 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132104 restraints weight = 20355.187| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.72 r_work: 0.3284 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17970 Z= 0.215 Angle : 0.607 9.717 24429 Z= 0.317 Chirality : 0.045 0.164 2652 Planarity : 0.005 0.040 3150 Dihedral : 5.495 74.932 2778 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.97 % Allowed : 12.98 % Favored : 84.05 % 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: 2.77 (0.27), residues: 351 sheet: 0.66 (0.22), residues: 555 loop : -0.26 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.010 0.002 HIS D 26 PHE 0.031 0.002 PHE A 118 TYR 0.024 0.002 TYR B 162 ARG 0.009 0.001 ARG K 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 15) link_NAG-ASN : angle 2.06814 ( 45) link_BETA1-4 : bond 0.00148 ( 3) link_BETA1-4 : angle 1.38083 ( 9) hydrogen bonds : bond 0.04748 ( 722) hydrogen bonds : angle 5.22442 ( 2043) SS BOND : bond 0.00572 ( 24) SS BOND : angle 1.59000 ( 48) covalent geometry : bond 0.00523 (17928) covalent geometry : angle 0.59739 (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 249 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8161 (tppt) REVERT: B 113 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8531 (m) REVERT: B 116 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8264 (ttmm) REVERT: C 21 ASN cc_start: 0.7812 (p0) cc_final: 0.7465 (p0) REVERT: C 144 LYS cc_start: 0.7963 (ptmm) cc_final: 0.7275 (mmmt) REVERT: C 246 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 103 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7884 (mt-10) REVERT: D 116 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8076 (ttmm) REVERT: G 32 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7721 (tppt) REVERT: G 60 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7748 (tm-30) REVERT: G 144 LYS cc_start: 0.7809 (ptmm) cc_final: 0.7269 (mmmt) REVERT: G 285 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7916 (mm-40) REVERT: H 100 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8456 (mt-10) REVERT: I 72 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7663 (ptmt) REVERT: I 116 LYS cc_start: 0.8329 (mtpm) cc_final: 0.7850 (ttmm) REVERT: J 89 MET cc_start: 0.8327 (tpt) cc_final: 0.7895 (tpt) outliers start: 56 outliers final: 34 residues processed: 225 average time/residue: 1.4206 time to fit residues: 360.6601 Evaluate side-chains 217 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 2.063 ------------------------------------------------------------------------------- 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 307 LYS 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 C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132786 restraints weight = 20303.047| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.60 r_work: 0.3265 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17970 Z= 0.176 Angle : 0.574 9.923 24429 Z= 0.300 Chirality : 0.044 0.155 2652 Planarity : 0.005 0.068 3150 Dihedral : 5.362 72.557 2778 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.76 % Allowed : 13.67 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2181 helix: 2.77 (0.27), residues: 357 sheet: 0.65 (0.21), residues: 579 loop : -0.25 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 36 HIS 0.009 0.001 HIS I 26 PHE 0.025 0.002 PHE C 118 TYR 0.024 0.001 TYR B 162 ARG 0.016 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 15) link_NAG-ASN : angle 1.88718 ( 45) link_BETA1-4 : bond 0.00180 ( 3) link_BETA1-4 : angle 1.37298 ( 9) hydrogen bonds : bond 0.04499 ( 722) hydrogen bonds : angle 5.17665 ( 2043) SS BOND : bond 0.00586 ( 24) SS BOND : angle 1.82855 ( 48) covalent geometry : bond 0.00424 (17928) covalent geometry : angle 0.56285 (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 245 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8617 (m) REVERT: B 116 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8361 (ttmm) REVERT: C 21 ASN cc_start: 0.7825 (p0) cc_final: 0.7551 (p0) REVERT: C 144 LYS cc_start: 0.7898 (ptmm) cc_final: 0.7429 (mmmt) REVERT: C 246 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7511 (mt-10) REVERT: D 116 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8139 (ttmm) REVERT: E 61 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7430 (tp40) REVERT: G 60 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7552 (tm-30) REVERT: G 144 LYS cc_start: 0.7752 (ptmm) cc_final: 0.7431 (mmmt) REVERT: G 285 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7871 (mm-40) REVERT: G 310 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7768 (ptp90) REVERT: I 72 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7707 (ptmt) REVERT: I 116 LYS cc_start: 0.8376 (mtpm) cc_final: 0.8049 (ttmm) REVERT: J 63 PHE cc_start: 0.8099 (m-80) cc_final: 0.7684 (m-80) REVERT: K 29 ASN cc_start: 0.8751 (m110) cc_final: 0.8313 (m-40) outliers start: 52 outliers final: 34 residues processed: 223 average time/residue: 1.2256 time to fit residues: 309.2623 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 : 3.822 ------------------------------------------------------------------------------- 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 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 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 164 LEU 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 167 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 111 optimal weight: 0.0040 chunk 58 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129659 restraints weight = 20170.758| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.71 r_work: 0.3151 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17970 Z= 0.130 Angle : 0.543 9.162 24429 Z= 0.285 Chirality : 0.043 0.150 2652 Planarity : 0.004 0.078 3150 Dihedral : 5.201 70.448 2778 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.12 % Allowed : 14.15 % Favored : 83.73 % 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: 0.78 (0.18), residues: 2181 helix: 2.73 (0.27), residues: 363 sheet: 0.65 (0.21), residues: 579 loop : -0.18 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.010 0.001 HIS I 26 PHE 0.020 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 0.00209 ( 15) link_NAG-ASN : angle 1.68949 ( 45) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 1.26620 ( 9) hydrogen bonds : bond 0.04212 ( 722) hydrogen bonds : angle 5.08100 ( 2043) SS BOND : bond 0.00541 ( 24) SS BOND : angle 1.53965 ( 48) covalent geometry : bond 0.00303 (17928) covalent geometry : angle 0.53440 (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 234 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7444 (mt-10) REVERT: B 113 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8116 (m) REVERT: B 116 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7668 (ttmm) REVERT: C 144 LYS cc_start: 0.7741 (ptmm) cc_final: 0.6891 (mmmt) REVERT: C 246 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 116 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7510 (ttmm) REVERT: E 61 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7762 (tp40) REVERT: E 100 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8602 (mt-10) REVERT: F 29 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6540 (p0) REVERT: F 92 ASP cc_start: 0.8049 (t70) cc_final: 0.7788 (t70) REVERT: G 60 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7726 (tm-30) REVERT: G 144 LYS cc_start: 0.7544 (ptmm) cc_final: 0.6792 (mmmt) REVERT: G 310 ARG cc_start: 0.8117 (mtm180) cc_final: 0.7768 (ptp90) REVERT: H 50 ARG cc_start: 0.8492 (ptt90) cc_final: 0.7893 (ptt180) REVERT: I 72 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7639 (ptmt) REVERT: J 63 PHE cc_start: 0.7778 (m-80) cc_final: 0.7310 (m-80) REVERT: J 89 MET cc_start: 0.8006 (tpt) cc_final: 0.7348 (tpt) REVERT: K 29 ASN cc_start: 0.8545 (m110) cc_final: 0.8113 (m110) outliers start: 40 outliers final: 23 residues processed: 217 average time/residue: 1.5569 time to fit residues: 383.6312 Evaluate side-chains 205 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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 C residue 78 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain 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 F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU 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 J residue 21 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 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: 4.9990 chunk 203 optimal weight: 8.9990 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: 2.9990 chunk 57 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS I 62 GLN L 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128634 restraints weight = 20421.017| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.60 r_work: 0.3091 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17970 Z= 0.295 Angle : 0.687 9.799 24429 Z= 0.354 Chirality : 0.048 0.157 2652 Planarity : 0.005 0.046 3150 Dihedral : 5.703 69.451 2778 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.54 % Allowed : 14.47 % Favored : 82.99 % 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: 0.53 (0.18), residues: 2181 helix: 2.56 (0.27), residues: 357 sheet: 0.70 (0.22), residues: 549 loop : -0.45 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 84 HIS 0.010 0.002 HIS H 100E PHE 0.035 0.003 PHE A 118 TYR 0.027 0.002 TYR B 162 ARG 0.010 0.001 ARG K 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 15) link_NAG-ASN : angle 2.39646 ( 45) link_BETA1-4 : bond 0.00253 ( 3) link_BETA1-4 : angle 1.72409 ( 9) hydrogen bonds : bond 0.05094 ( 722) hydrogen bonds : angle 5.38632 ( 2043) SS BOND : bond 0.00664 ( 24) SS BOND : angle 1.73990 ( 48) covalent geometry : bond 0.00721 (17928) covalent geometry : angle 0.67541 (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 243 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8336 (m) REVERT: C 144 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7033 (mmmt) REVERT: C 246 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 72 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7547 (pttt) REVERT: D 116 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7823 (ttmm) REVERT: E 61 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7655 (tp40) REVERT: G 60 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7808 (tm-30) REVERT: G 144 LYS cc_start: 0.7753 (ptmm) cc_final: 0.7085 (mmmt) REVERT: G 285 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7940 (mm-40) REVERT: I 11 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: J 63 PHE cc_start: 0.7945 (m-80) cc_final: 0.7472 (m-80) REVERT: J 89 MET cc_start: 0.8218 (tpt) cc_final: 0.7735 (tpt) REVERT: K 29 ASN cc_start: 0.8963 (m110) cc_final: 0.8505 (m-40) outliers start: 48 outliers final: 35 residues processed: 223 average time/residue: 1.5623 time to fit residues: 397.6584 Evaluate side-chains 228 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 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 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 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 11 GLU 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 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: 0.8980 chunk 59 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS I 60 ASN L 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128171 restraints weight = 20255.148| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.58 r_work: 0.3116 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5031 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= 0.148 Angle : 0.560 7.899 24429 Z= 0.293 Chirality : 0.043 0.152 2652 Planarity : 0.005 0.081 3150 Dihedral : 5.292 66.779 2778 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.07 % Allowed : 15.42 % Favored : 82.51 % 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: 0.59 (0.18), residues: 2181 helix: 2.70 (0.27), residues: 363 sheet: 0.60 (0.20), residues: 609 loop : -0.43 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.009 0.001 HIS I 26 PHE 0.021 0.002 PHE C 118 TYR 0.024 0.001 TYR B 162 ARG 0.017 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 15) link_NAG-ASN : angle 1.82516 ( 45) link_BETA1-4 : bond 0.00247 ( 3) link_BETA1-4 : angle 1.40026 ( 9) hydrogen bonds : bond 0.04331 ( 722) hydrogen bonds : angle 5.21206 ( 2043) SS BOND : bond 0.00496 ( 24) SS BOND : angle 1.41250 ( 48) covalent geometry : bond 0.00351 (17928) covalent geometry : angle 0.55178 (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: 39 poor density : 199 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ASN cc_start: 0.8453 (t0) cc_final: 0.8154 (m-40) REVERT: B 103 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7572 (mt-10) REVERT: B 105 GLU cc_start: 0.7844 (tt0) cc_final: 0.7253 (tp30) REVERT: B 113 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8132 (m) REVERT: B 116 LYS cc_start: 0.8022 (mtpm) cc_final: 0.7448 (ttmm) REVERT: C 144 LYS cc_start: 0.7780 (ptmm) cc_final: 0.6900 (mmmt) REVERT: C 149 ARG cc_start: 0.8526 (mtm180) cc_final: 0.8220 (mtp180) REVERT: C 246 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7675 (mt-10) REVERT: D 72 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7748 (pttt) REVERT: D 106 ARG cc_start: 0.7548 (mmp80) cc_final: 0.7177 (mtp-110) REVERT: D 116 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7571 (ttmm) REVERT: E 61 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7613 (tp40) REVERT: E 100 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8672 (mt-10) REVERT: G 60 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7911 (tm-30) REVERT: G 285 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7725 (mm-40) REVERT: H 50 ARG cc_start: 0.8667 (ptt90) cc_final: 0.8012 (ptt180) REVERT: I 72 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7690 (ptmt) REVERT: J 63 PHE cc_start: 0.7870 (m-80) cc_final: 0.7342 (m-80) REVERT: J 89 MET cc_start: 0.8159 (tpt) cc_final: 0.7597 (tpt) REVERT: K 29 ASN cc_start: 0.8770 (m110) cc_final: 0.8246 (m-40) outliers start: 39 outliers final: 28 residues processed: 219 average time/residue: 1.2584 time to fit residues: 310.2950 Evaluate side-chains 214 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 148 CYS 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 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 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 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 119 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 201 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 chunk 113 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 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 I 26 HIS L 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 130)---------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130344 restraints weight = 20219.921| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.56 r_work: 0.3158 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17970 Z= 0.128 Angle : 0.536 7.339 24429 Z= 0.281 Chirality : 0.042 0.150 2652 Planarity : 0.005 0.092 3150 Dihedral : 4.866 53.383 2778 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.07 % Allowed : 15.90 % Favored : 82.03 % 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: 0.71 (0.18), residues: 2181 helix: 2.79 (0.27), residues: 363 sheet: 0.65 (0.21), residues: 609 loop : -0.34 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.011 0.001 HIS D 26 PHE 0.019 0.001 PHE C 118 TYR 0.024 0.001 TYR I 162 ARG 0.018 0.001 ARG L 95A Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 15) link_NAG-ASN : angle 1.69516 ( 45) link_BETA1-4 : bond 0.00222 ( 3) link_BETA1-4 : angle 1.26653 ( 9) hydrogen bonds : bond 0.04073 ( 722) hydrogen bonds : angle 5.08695 ( 2043) SS BOND : bond 0.00450 ( 24) SS BOND : angle 1.25953 ( 48) covalent geometry : bond 0.00299 (17928) covalent geometry : angle 0.52858 (24327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16247.03 seconds wall clock time: 285 minutes 16.13 seconds (17116.13 seconds total)