Starting phenix.real_space_refine on Mon Apr 6 09:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7t_49099/04_2026/9n7t_49099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7t_49099/04_2026/9n7t_49099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n7t_49099/04_2026/9n7t_49099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7t_49099/04_2026/9n7t_49099.map" model { file = "/net/cci-nas-00/data/ceres_data/9n7t_49099/04_2026/9n7t_49099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7t_49099/04_2026/9n7t_49099.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10860 2.51 5 N 2934 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17262 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2530 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 959 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "a" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1380 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "B" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2530 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain: "F" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 959 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1380 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2530 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain: "G" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 959 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1380 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.84, per 1000 atoms: 0.22 Number of scatterers: 17262 At special positions: 0 Unit cell: (138.475, 132.675, 145.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3381 8.00 N 2934 7.00 C 10860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 148 " 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 K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A 401 " - " ASN A 169 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 21 " " NAG B 401 " - " ASN B 169 " " NAG B 402 " - " ASN B 33 " " NAG B 403 " - " ASN B 21 " " NAG C 401 " - " ASN C 169 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 21 " " NAG K 1 " - " ASN A 289 " " NAG M 1 " - " ASN a 154 " " NAG N 1 " - " ASN B 289 " " NAG O 1 " - " ASN I 154 " " NAG P 1 " - " ASN C 289 " " NAG Q 1 " - " ASN J 154 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 731.9 milliseconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 53 sheets defined 21.6% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.903A pdb=" N GLU A 78 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.522A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.571A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'a' and resid 37 through 58 Processing helix chain 'a' and resid 74 through 127 Processing helix chain 'a' and resid 145 through 155 Processing helix chain 'a' and resid 158 through 170 removed outlier: 3.931A pdb=" N TYR a 162 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU a 164 " --> pdb=" O PRO a 160 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU a 165 " --> pdb=" O GLN a 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 4.903A pdb=" N GLU B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.524A pdb=" N TRP B 127 " --> pdb=" O LYS B 125A" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.571A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' 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 155 Processing helix chain 'I' and resid 158 through 170 removed outlier: 3.931A pdb=" N TYR I 162 " --> pdb=" O TYR I 158 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU I 165 " --> pdb=" O GLN I 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.904A pdb=" N GLU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 removed outlier: 3.522A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.569A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'J' and resid 37 through 58 Processing helix chain 'J' and resid 74 through 127 Processing helix chain 'J' and resid 145 through 155 Processing helix chain 'J' and resid 158 through 170 removed outlier: 3.932A pdb=" N TYR J 162 " --> pdb=" O TYR J 158 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU J 165 " --> pdb=" O GLN J 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.610A pdb=" N GLY a 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.147A pdb=" N LEU A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.511A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.444A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.444A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.546A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 287 through 288 removed outlier: 4.155A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.528A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.055A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.786A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR H 100F" --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N ILE H 98 " --> pdb=" O GLY H 100D" (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLY H 100D" --> pdb=" O ILE H 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AC2, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.617A pdb=" N GLY I 23 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AC5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.145A pdb=" N LEU B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.513A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.436A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.436A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AD2, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.544A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD4, first strand: chain 'B' and resid 287 through 288 removed outlier: 4.156A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AD6, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.531A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.054A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.788A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR D 100F" --> pdb=" O ASN D 96 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N ILE D 98 " --> pdb=" O GLY D 100D" (cutoff:3.500A) removed outlier: 9.201A pdb=" N GLY D 100D" --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 31 through 36 removed outlier: 3.616A pdb=" N GLY J 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS J 25 " --> pdb=" O CYS C 14 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN C 12 " --> pdb=" O SER J 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AE4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AE5, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.146A pdb=" N LEU C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.512A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.436A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.436A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AF1, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.546A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AF3, first strand: chain 'C' and resid 287 through 288 removed outlier: 4.155A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AF5, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.531A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.051A pdb=" N MET E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.783A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR E 100F" --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N ILE E 98 " --> pdb=" O GLY E 100D" (cutoff:3.500A) removed outlier: 9.201A pdb=" N GLY E 100D" --> pdb=" O ILE E 98 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1881 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: 3.06 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5555 1.34 - 1.46: 3999 1.46 - 1.58: 7975 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 17655 Sorted by residual: bond pdb=" C ASN L 53 " pdb=" N ARG L 54 " ideal model delta sigma weight residual 1.333 1.383 -0.050 2.74e-02 1.33e+03 3.38e+00 bond pdb=" N SER A 10 " pdb=" CA SER A 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N SER B 10 " pdb=" CA SER B 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N SER C 10 " pdb=" CA SER C 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 17650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 23396 1.93 - 3.86: 434 3.86 - 5.79: 101 5.79 - 7.72: 0 7.72 - 9.65: 3 Bond angle restraints: 23934 Sorted by residual: angle pdb=" N ASN a 60 " pdb=" CA ASN a 60 " pdb=" C ASN a 60 " ideal model delta sigma weight residual 113.55 108.59 4.96 1.26e+00 6.30e-01 1.55e+01 angle pdb=" N ASN J 60 " pdb=" CA ASN J 60 " pdb=" C ASN J 60 " ideal model delta sigma weight residual 113.55 108.60 4.95 1.26e+00 6.30e-01 1.55e+01 angle pdb=" N ASN I 60 " pdb=" CA ASN I 60 " pdb=" C ASN I 60 " ideal model delta sigma weight residual 113.55 108.63 4.92 1.26e+00 6.30e-01 1.52e+01 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 125.95 -9.65 3.50e+00 8.16e-02 7.60e+00 angle pdb=" CA LEU C 61 " pdb=" CB LEU C 61 " pdb=" CG LEU C 61 " ideal model delta sigma weight residual 116.30 125.94 -9.64 3.50e+00 8.16e-02 7.59e+00 ... (remaining 23929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 9800 15.50 - 31.00: 737 31.00 - 46.50: 140 46.50 - 62.00: 36 62.00 - 77.49: 6 Dihedral angle restraints: 10719 sinusoidal: 4527 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.30 37.30 1 1.00e+01 1.00e-02 1.96e+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 -123.22 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS B 64 " pdb=" SG CYS B 64 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.20 37.20 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 10716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1498 0.032 - 0.065: 797 0.065 - 0.097: 158 0.097 - 0.129: 120 0.129 - 0.161: 64 Chirality restraints: 2637 Sorted by residual: chirality pdb=" CA VAL C 214 " pdb=" N VAL C 214 " pdb=" C VAL C 214 " pdb=" CB VAL C 214 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA VAL A 214 " pdb=" N VAL A 214 " pdb=" C VAL A 214 " pdb=" CB VAL A 214 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA VAL B 214 " pdb=" N VAL B 214 " pdb=" C VAL B 214 " pdb=" CB VAL B 214 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 2634 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 73 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 74 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 73 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 74 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 73 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 74 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.029 5.00e-02 4.00e+02 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 303 2.69 - 3.24: 16079 3.24 - 3.79: 26577 3.79 - 4.35: 39128 4.35 - 4.90: 64634 Nonbonded interactions: 146721 Sorted by model distance: nonbonded pdb=" O ASP G 27B" pdb=" OG SER G 90 " model vdw 2.133 3.040 nonbonded pdb=" O ASP F 27B" pdb=" OG SER F 90 " model vdw 2.134 3.040 nonbonded pdb=" O ASP L 27B" pdb=" OG SER L 90 " model vdw 2.134 3.040 nonbonded pdb=" O PRO B 125 " pdb=" OG SER B 126 " model vdw 2.227 3.040 nonbonded pdb=" O PRO A 125 " pdb=" OG SER A 126 " model vdw 2.228 3.040 ... (remaining 146716 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 7.400 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.005 0.067 17697 Z= 0.181 Angle : 0.705 9.648 24039 Z= 0.366 Chirality : 0.047 0.161 2637 Planarity : 0.005 0.051 3066 Dihedral : 11.293 77.495 6726 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2130 helix: 2.35 (0.27), residues: 354 sheet: -0.60 (0.23), residues: 489 loop : -0.91 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 127 TYR 0.015 0.002 TYR D 33 PHE 0.017 0.002 PHE A 118 TRP 0.007 0.001 TRP J 92 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00451 (17655) covalent geometry : angle 0.69486 (23934) SS BOND : bond 0.00243 ( 21) SS BOND : angle 1.47652 ( 42) hydrogen bonds : bond 0.14960 ( 683) hydrogen bonds : angle 7.05304 ( 1881) link_BETA1-4 : bond 0.00313 ( 6) link_BETA1-4 : angle 1.11137 ( 18) link_NAG-ASN : bond 0.00351 ( 15) link_NAG-ASN : angle 2.41028 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 CYS cc_start: 0.8534 (m) cc_final: 0.8316 (m) REVERT: A 75 MET cc_start: 0.8634 (mmm) cc_final: 0.8424 (mmt) REVERT: A 174 GLU cc_start: 0.7738 (mp0) cc_final: 0.7363 (mm-30) REVERT: A 264 ASP cc_start: 0.7583 (t70) cc_final: 0.7343 (m-30) REVERT: A 280 LYS cc_start: 0.8535 (pttm) cc_final: 0.8012 (mtpp) REVERT: A 304 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7888 (mp0) REVERT: L 45 LYS cc_start: 0.8637 (tttt) cc_final: 0.8274 (tttm) REVERT: L 72 SER cc_start: 0.8623 (m) cc_final: 0.7876 (p) REVERT: H 3 GLN cc_start: 0.8227 (pt0) cc_final: 0.8002 (pp30) REVERT: a 17 MET cc_start: 0.8866 (ttm) cc_final: 0.8563 (ttm) REVERT: a 27 SER cc_start: 0.8741 (m) cc_final: 0.8294 (t) REVERT: a 72 ASN cc_start: 0.8118 (t0) cc_final: 0.7814 (t0) REVERT: a 77 ILE cc_start: 0.8894 (mm) cc_final: 0.8583 (mm) REVERT: a 102 MET cc_start: 0.8491 (mtt) cc_final: 0.8267 (mtm) REVERT: a 137 CYS cc_start: 0.8593 (m) cc_final: 0.7812 (m) REVERT: a 161 GLN cc_start: 0.8892 (tt0) cc_final: 0.8417 (tt0) REVERT: a 163 SER cc_start: 0.8804 (t) cc_final: 0.8604 (p) REVERT: B 14 CYS cc_start: 0.8556 (m) cc_final: 0.8287 (m) REVERT: B 41 ASP cc_start: 0.8613 (t0) cc_final: 0.8384 (t0) REVERT: B 190 GLU cc_start: 0.7325 (tt0) cc_final: 0.7114 (tt0) REVERT: B 208 THR cc_start: 0.8662 (p) cc_final: 0.8429 (t) REVERT: B 264 ASP cc_start: 0.7573 (t70) cc_final: 0.7325 (m-30) REVERT: B 304 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7673 (mp0) REVERT: F 45 LYS cc_start: 0.8645 (tttt) cc_final: 0.8338 (tttm) REVERT: F 72 SER cc_start: 0.8575 (m) cc_final: 0.7810 (p) REVERT: I 17 MET cc_start: 0.8869 (ttm) cc_final: 0.8576 (ttm) REVERT: I 72 ASN cc_start: 0.8150 (t0) cc_final: 0.7841 (t0) REVERT: I 77 ILE cc_start: 0.8917 (mm) cc_final: 0.8587 (mm) REVERT: I 102 MET cc_start: 0.8469 (mtt) cc_final: 0.8249 (mtm) REVERT: I 137 CYS cc_start: 0.8604 (m) cc_final: 0.7898 (m) REVERT: I 161 GLN cc_start: 0.8911 (tt0) cc_final: 0.8445 (tt0) REVERT: C 14 CYS cc_start: 0.8559 (m) cc_final: 0.8257 (m) REVERT: C 264 ASP cc_start: 0.7621 (t70) cc_final: 0.7374 (m-30) REVERT: C 280 LYS cc_start: 0.8477 (pttm) cc_final: 0.7953 (mtpp) REVERT: C 304 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7860 (mp0) REVERT: J 72 ASN cc_start: 0.8061 (t0) cc_final: 0.7786 (t0) REVERT: J 74 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8039 (mt-10) REVERT: J 77 ILE cc_start: 0.8883 (mm) cc_final: 0.8576 (mm) REVERT: J 82 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8202 (ttmm) REVERT: J 102 MET cc_start: 0.8494 (mtt) cc_final: 0.8275 (mtm) REVERT: J 137 CYS cc_start: 0.8627 (m) cc_final: 0.8008 (m) REVERT: J 161 GLN cc_start: 0.8925 (tt0) cc_final: 0.8321 (tt0) REVERT: J 163 SER cc_start: 0.8819 (t) cc_final: 0.8595 (p) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1516 time to fit residues: 99.6891 Evaluate side-chains 335 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN a 125 GLN B 172 ASN B 278 ASN F 6 GLN I 125 GLN C 278 ASN G 6 GLN E 76 ASN J 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105606 restraints weight = 20631.601| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.69 r_work: 0.2911 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17697 Z= 0.191 Angle : 0.579 8.921 24039 Z= 0.295 Chirality : 0.045 0.161 2637 Planarity : 0.005 0.049 3066 Dihedral : 6.250 54.696 2793 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.48 % Allowed : 5.97 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2130 helix: 2.66 (0.26), residues: 354 sheet: -0.31 (0.23), residues: 477 loop : -0.82 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 71 TYR 0.019 0.002 TYR E 33 PHE 0.016 0.002 PHE B 118 TRP 0.010 0.001 TRP a 92 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00455 (17655) covalent geometry : angle 0.56960 (23934) SS BOND : bond 0.00313 ( 21) SS BOND : angle 0.90300 ( 42) hydrogen bonds : bond 0.04221 ( 683) hydrogen bonds : angle 5.50766 ( 1881) link_BETA1-4 : bond 0.00256 ( 6) link_BETA1-4 : angle 1.49790 ( 18) link_NAG-ASN : bond 0.00383 ( 15) link_NAG-ASN : angle 2.25611 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 333 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8296 (mmp80) cc_final: 0.8066 (mmp-170) REVERT: A 174 GLU cc_start: 0.8011 (mp0) cc_final: 0.7616 (mm-30) REVERT: A 278 ASN cc_start: 0.8665 (t0) cc_final: 0.8400 (t0) REVERT: A 304 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8143 (mp0) REVERT: L 72 SER cc_start: 0.8582 (m) cc_final: 0.7899 (p) REVERT: a 17 MET cc_start: 0.8959 (ttm) cc_final: 0.8746 (ttm) REVERT: a 57 ASP cc_start: 0.8410 (m-30) cc_final: 0.8193 (m-30) REVERT: a 77 ILE cc_start: 0.9218 (mm) cc_final: 0.8979 (mm) REVERT: a 137 CYS cc_start: 0.8825 (m) cc_final: 0.8044 (m) REVERT: B 63 ASP cc_start: 0.7820 (p0) cc_final: 0.7522 (t0) REVERT: B 304 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8175 (mp0) REVERT: F 72 SER cc_start: 0.8596 (m) cc_final: 0.7920 (p) REVERT: I 17 MET cc_start: 0.8953 (ttm) cc_final: 0.8745 (ttm) REVERT: I 57 ASP cc_start: 0.8285 (m-30) cc_final: 0.7922 (m-30) REVERT: I 77 ILE cc_start: 0.9203 (mm) cc_final: 0.8956 (mm) REVERT: I 102 MET cc_start: 0.8607 (mtt) cc_final: 0.8308 (mtm) REVERT: I 137 CYS cc_start: 0.8722 (m) cc_final: 0.8037 (m) REVERT: C 14 CYS cc_start: 0.8661 (m) cc_final: 0.8396 (m) REVERT: C 304 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8141 (mp0) REVERT: J 77 ILE cc_start: 0.9203 (mm) cc_final: 0.8949 (mm) REVERT: J 137 CYS cc_start: 0.8839 (m) cc_final: 0.8320 (m) REVERT: J 161 GLN cc_start: 0.8743 (tt0) cc_final: 0.8538 (tt0) outliers start: 9 outliers final: 8 residues processed: 334 average time/residue: 0.1733 time to fit residues: 81.4103 Evaluate side-chains 294 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 286 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain J residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 74 optimal weight: 0.0770 chunk 204 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN L 37 GLN a 125 GLN a 161 GLN I 125 GLN C 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106341 restraints weight = 20849.387| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.61 r_work: 0.2986 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17697 Z= 0.171 Angle : 0.534 6.052 24039 Z= 0.273 Chirality : 0.043 0.158 2637 Planarity : 0.004 0.049 3066 Dihedral : 6.178 54.223 2793 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.34 % Allowed : 8.98 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2130 helix: 2.76 (0.27), residues: 354 sheet: -0.17 (0.23), residues: 492 loop : -0.81 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 167 TYR 0.017 0.001 TYR E 33 PHE 0.013 0.002 PHE a 9 TRP 0.009 0.001 TRP a 92 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00407 (17655) covalent geometry : angle 0.52491 (23934) SS BOND : bond 0.00309 ( 21) SS BOND : angle 0.76048 ( 42) hydrogen bonds : bond 0.03919 ( 683) hydrogen bonds : angle 5.32013 ( 1881) link_BETA1-4 : bond 0.00304 ( 6) link_BETA1-4 : angle 1.24394 ( 18) link_NAG-ASN : bond 0.00416 ( 15) link_NAG-ASN : angle 2.18695 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8211 (mmp80) cc_final: 0.7976 (mmp-170) REVERT: A 174 GLU cc_start: 0.7938 (mp0) cc_final: 0.7469 (mm-30) REVERT: A 258 TYR cc_start: 0.8931 (m-80) cc_final: 0.8586 (m-80) REVERT: A 304 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8016 (mp0) REVERT: a 17 MET cc_start: 0.9028 (ttm) cc_final: 0.8754 (ttm) REVERT: a 57 ASP cc_start: 0.8419 (m-30) cc_final: 0.8173 (m-30) REVERT: a 77 ILE cc_start: 0.9125 (mm) cc_final: 0.8876 (mm) REVERT: B 63 ASP cc_start: 0.7708 (p0) cc_final: 0.7373 (t0) REVERT: I 17 MET cc_start: 0.9028 (ttm) cc_final: 0.8741 (ttm) REVERT: I 57 ASP cc_start: 0.8342 (m-30) cc_final: 0.8047 (m-30) REVERT: I 77 ILE cc_start: 0.9110 (mm) cc_final: 0.8846 (mm) REVERT: I 102 MET cc_start: 0.8538 (mtt) cc_final: 0.8242 (mtm) REVERT: I 161 GLN cc_start: 0.8776 (tt0) cc_final: 0.8573 (tt0) REVERT: C 14 CYS cc_start: 0.8667 (m) cc_final: 0.8288 (m) REVERT: C 304 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8023 (mp0) REVERT: J 77 ILE cc_start: 0.9093 (mm) cc_final: 0.8853 (mm) REVERT: J 102 MET cc_start: 0.8508 (mtt) cc_final: 0.8247 (mtm) REVERT: J 137 CYS cc_start: 0.8763 (m) cc_final: 0.8096 (m) REVERT: J 161 GLN cc_start: 0.8744 (tt0) cc_final: 0.8504 (tt0) outliers start: 25 outliers final: 9 residues processed: 308 average time/residue: 0.1640 time to fit residues: 71.8517 Evaluate side-chains 289 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 280 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN L 37 GLN a 125 GLN I 125 GLN C 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104241 restraints weight = 20788.309| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.57 r_work: 0.2935 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17697 Z= 0.194 Angle : 0.542 10.694 24039 Z= 0.276 Chirality : 0.044 0.167 2637 Planarity : 0.004 0.048 3066 Dihedral : 6.206 54.093 2793 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.45 % Allowed : 10.22 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2130 helix: 2.74 (0.26), residues: 354 sheet: -0.15 (0.23), residues: 492 loop : -0.82 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 64 TYR 0.017 0.001 TYR E 33 PHE 0.014 0.002 PHE C 79 TRP 0.009 0.001 TRP a 92 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00462 (17655) covalent geometry : angle 0.53265 (23934) SS BOND : bond 0.00354 ( 21) SS BOND : angle 0.69696 ( 42) hydrogen bonds : bond 0.03871 ( 683) hydrogen bonds : angle 5.26395 ( 1881) link_BETA1-4 : bond 0.00341 ( 6) link_BETA1-4 : angle 1.29583 ( 18) link_NAG-ASN : bond 0.00354 ( 15) link_NAG-ASN : angle 2.15562 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8253 (mmp80) cc_final: 0.8020 (mmp-170) REVERT: A 174 GLU cc_start: 0.7986 (mp0) cc_final: 0.7547 (mm-30) REVERT: A 258 TYR cc_start: 0.8927 (m-80) cc_final: 0.8623 (m-80) REVERT: a 17 MET cc_start: 0.8998 (ttm) cc_final: 0.8733 (ttm) REVERT: a 57 ASP cc_start: 0.8323 (m-30) cc_final: 0.8102 (m-30) REVERT: a 77 ILE cc_start: 0.9218 (mm) cc_final: 0.8926 (mm) REVERT: a 102 MET cc_start: 0.8622 (mtt) cc_final: 0.8332 (mtm) REVERT: B 63 ASP cc_start: 0.7785 (p0) cc_final: 0.7451 (t0) REVERT: I 17 MET cc_start: 0.9006 (ttm) cc_final: 0.8765 (ttm) REVERT: I 57 ASP cc_start: 0.8330 (m-30) cc_final: 0.7954 (m-30) REVERT: I 77 ILE cc_start: 0.9186 (mm) cc_final: 0.8918 (mm) REVERT: I 102 MET cc_start: 0.8567 (mtt) cc_final: 0.8316 (mtm) REVERT: I 161 GLN cc_start: 0.8778 (tt0) cc_final: 0.8497 (tt0) REVERT: C 14 CYS cc_start: 0.8746 (m) cc_final: 0.8351 (m) REVERT: C 304 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8085 (mp0) REVERT: E 66 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8572 (mtm110) REVERT: J 57 ASP cc_start: 0.8292 (m-30) cc_final: 0.8071 (m-30) REVERT: J 77 ILE cc_start: 0.9192 (mm) cc_final: 0.8935 (mm) REVERT: J 137 CYS cc_start: 0.8692 (m) cc_final: 0.8023 (m) REVERT: J 161 GLN cc_start: 0.8754 (tt0) cc_final: 0.8526 (tt0) outliers start: 27 outliers final: 14 residues processed: 298 average time/residue: 0.1632 time to fit residues: 69.0519 Evaluate side-chains 289 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 275 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 164 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN L 37 GLN a 125 GLN B 150 ASN I 125 GLN C 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.095660 restraints weight = 21214.409| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.76 r_work: 0.2883 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17697 Z= 0.257 Angle : 0.588 8.961 24039 Z= 0.300 Chirality : 0.046 0.161 2637 Planarity : 0.004 0.047 3066 Dihedral : 6.401 54.618 2793 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.04 % Allowed : 10.81 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2130 helix: 2.56 (0.26), residues: 354 sheet: -0.21 (0.23), residues: 477 loop : -0.88 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 227 TYR 0.020 0.002 TYR E 33 PHE 0.016 0.002 PHE B 79 TRP 0.010 0.001 TRP a 92 HIS 0.007 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00615 (17655) covalent geometry : angle 0.57746 (23934) SS BOND : bond 0.00466 ( 21) SS BOND : angle 0.78018 ( 42) hydrogen bonds : bond 0.04126 ( 683) hydrogen bonds : angle 5.39943 ( 1881) link_BETA1-4 : bond 0.00282 ( 6) link_BETA1-4 : angle 1.33207 ( 18) link_NAG-ASN : bond 0.00554 ( 15) link_NAG-ASN : angle 2.44635 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8318 (mmp80) cc_final: 0.8101 (mmp-170) REVERT: A 174 GLU cc_start: 0.8111 (mp0) cc_final: 0.7519 (mm-30) REVERT: A 258 TYR cc_start: 0.9004 (m-80) cc_final: 0.8662 (m-80) REVERT: a 17 MET cc_start: 0.9106 (ttm) cc_final: 0.8829 (ttm) REVERT: a 57 ASP cc_start: 0.8433 (m-30) cc_final: 0.8032 (m-30) REVERT: a 77 ILE cc_start: 0.9252 (mm) cc_final: 0.8956 (mm) REVERT: a 102 MET cc_start: 0.8805 (mtt) cc_final: 0.8537 (mtm) REVERT: B 63 ASP cc_start: 0.7769 (p0) cc_final: 0.7419 (t0) REVERT: I 17 MET cc_start: 0.9116 (ttm) cc_final: 0.8848 (ttm) REVERT: I 57 ASP cc_start: 0.8418 (m-30) cc_final: 0.7999 (m-30) REVERT: I 77 ILE cc_start: 0.9232 (mm) cc_final: 0.8898 (mm) REVERT: I 102 MET cc_start: 0.8766 (mtt) cc_final: 0.8517 (mtm) REVERT: I 161 GLN cc_start: 0.8819 (tt0) cc_final: 0.8504 (tt0) REVERT: C 14 CYS cc_start: 0.8870 (m) cc_final: 0.8455 (m) REVERT: C 174 GLU cc_start: 0.7994 (mp0) cc_final: 0.7454 (mm-30) REVERT: C 304 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7898 (tm-30) REVERT: G 21 ILE cc_start: 0.8380 (mt) cc_final: 0.8163 (mt) REVERT: E 3 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8487 (pp30) REVERT: J 57 ASP cc_start: 0.8411 (m-30) cc_final: 0.8187 (m-30) REVERT: J 77 ILE cc_start: 0.9209 (mm) cc_final: 0.8997 (mm) REVERT: J 102 MET cc_start: 0.8708 (mtt) cc_final: 0.8438 (mtm) REVERT: J 137 CYS cc_start: 0.8752 (m) cc_final: 0.8127 (m) REVERT: J 161 GLN cc_start: 0.8790 (tt0) cc_final: 0.8549 (tt0) outliers start: 38 outliers final: 29 residues processed: 294 average time/residue: 0.1621 time to fit residues: 67.9455 Evaluate side-chains 299 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 22 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 189 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.0470 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN L 37 GLN a 125 GLN I 125 GLN C 224 ASN J 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096780 restraints weight = 21093.539| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.81 r_work: 0.2874 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17697 Z= 0.189 Angle : 0.542 9.297 24039 Z= 0.277 Chirality : 0.044 0.157 2637 Planarity : 0.004 0.047 3066 Dihedral : 6.308 54.160 2793 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.77 % Allowed : 11.88 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2130 helix: 2.69 (0.26), residues: 354 sheet: -0.21 (0.23), residues: 477 loop : -0.84 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 167 TYR 0.017 0.001 TYR E 33 PHE 0.014 0.002 PHE B 79 TRP 0.009 0.001 TRP a 92 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00448 (17655) covalent geometry : angle 0.53284 (23934) SS BOND : bond 0.00407 ( 21) SS BOND : angle 0.67218 ( 42) hydrogen bonds : bond 0.03813 ( 683) hydrogen bonds : angle 5.27473 ( 1881) link_BETA1-4 : bond 0.00350 ( 6) link_BETA1-4 : angle 1.16137 ( 18) link_NAG-ASN : bond 0.00441 ( 15) link_NAG-ASN : angle 2.23101 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8330 (mmp80) cc_final: 0.8109 (mmp-170) REVERT: A 174 GLU cc_start: 0.8140 (mp0) cc_final: 0.7508 (mm-30) REVERT: A 258 TYR cc_start: 0.8991 (m-80) cc_final: 0.8713 (m-80) REVERT: a 17 MET cc_start: 0.9088 (ttm) cc_final: 0.8815 (ttm) REVERT: a 57 ASP cc_start: 0.8414 (m-30) cc_final: 0.8058 (m-30) REVERT: a 77 ILE cc_start: 0.9210 (mm) cc_final: 0.8920 (mm) REVERT: a 102 MET cc_start: 0.8788 (mtt) cc_final: 0.8483 (mtm) REVERT: B 63 ASP cc_start: 0.7771 (p0) cc_final: 0.7393 (t0) REVERT: I 17 MET cc_start: 0.9098 (ttm) cc_final: 0.8846 (ttm) REVERT: I 57 ASP cc_start: 0.8439 (m-30) cc_final: 0.8027 (m-30) REVERT: I 77 ILE cc_start: 0.9214 (mm) cc_final: 0.8933 (mm) REVERT: I 102 MET cc_start: 0.8761 (mtt) cc_final: 0.8499 (mtm) REVERT: I 161 GLN cc_start: 0.8811 (tt0) cc_final: 0.8508 (tt0) REVERT: C 14 CYS cc_start: 0.8864 (m) cc_final: 0.8450 (m) REVERT: C 174 GLU cc_start: 0.7982 (mp0) cc_final: 0.7313 (mm-30) REVERT: C 304 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7869 (tm-30) REVERT: E 3 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8472 (pp30) REVERT: J 57 ASP cc_start: 0.8397 (m-30) cc_final: 0.8182 (m-30) REVERT: J 77 ILE cc_start: 0.9178 (mm) cc_final: 0.8909 (mm) REVERT: J 137 CYS cc_start: 0.8774 (m) cc_final: 0.8107 (m) REVERT: J 161 GLN cc_start: 0.8767 (tt0) cc_final: 0.8526 (tt0) outliers start: 33 outliers final: 28 residues processed: 287 average time/residue: 0.1618 time to fit residues: 65.9055 Evaluate side-chains 298 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 22 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN L 37 GLN a 125 GLN I 125 GLN C 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096158 restraints weight = 21239.111| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.79 r_work: 0.2900 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17697 Z= 0.210 Angle : 0.550 9.192 24039 Z= 0.281 Chirality : 0.044 0.159 2637 Planarity : 0.004 0.046 3066 Dihedral : 6.332 54.344 2793 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.31 % Allowed : 11.77 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2130 helix: 2.66 (0.26), residues: 354 sheet: -0.20 (0.23), residues: 477 loop : -0.84 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 75 TYR 0.018 0.001 TYR E 33 PHE 0.014 0.002 PHE B 79 TRP 0.009 0.001 TRP a 92 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00500 (17655) covalent geometry : angle 0.54049 (23934) SS BOND : bond 0.00426 ( 21) SS BOND : angle 0.68587 ( 42) hydrogen bonds : bond 0.03864 ( 683) hydrogen bonds : angle 5.26306 ( 1881) link_BETA1-4 : bond 0.00310 ( 6) link_BETA1-4 : angle 1.17307 ( 18) link_NAG-ASN : bond 0.00417 ( 15) link_NAG-ASN : angle 2.24396 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8300 (mmp80) cc_final: 0.8087 (mmp-170) REVERT: A 174 GLU cc_start: 0.8165 (mp0) cc_final: 0.7510 (mm-30) REVERT: A 258 TYR cc_start: 0.8990 (m-80) cc_final: 0.8729 (m-80) REVERT: a 17 MET cc_start: 0.9075 (ttm) cc_final: 0.8803 (ttm) REVERT: a 57 ASP cc_start: 0.8410 (m-30) cc_final: 0.8061 (m-30) REVERT: a 77 ILE cc_start: 0.9238 (mm) cc_final: 0.8965 (mm) REVERT: a 102 MET cc_start: 0.8802 (mtt) cc_final: 0.8500 (mtm) REVERT: B 63 ASP cc_start: 0.7831 (p0) cc_final: 0.7454 (t0) REVERT: I 17 MET cc_start: 0.9088 (ttm) cc_final: 0.8825 (ttm) REVERT: I 57 ASP cc_start: 0.8417 (m-30) cc_final: 0.8009 (m-30) REVERT: I 77 ILE cc_start: 0.9237 (mm) cc_final: 0.8943 (mm) REVERT: I 102 MET cc_start: 0.8761 (mtt) cc_final: 0.8512 (mtm) REVERT: I 161 GLN cc_start: 0.8825 (tt0) cc_final: 0.8523 (tt0) REVERT: C 14 CYS cc_start: 0.8842 (m) cc_final: 0.8428 (m) REVERT: E 3 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8497 (pp30) REVERT: J 57 ASP cc_start: 0.8398 (m-30) cc_final: 0.8178 (m-30) REVERT: J 137 CYS cc_start: 0.8750 (m) cc_final: 0.8088 (m) REVERT: J 161 GLN cc_start: 0.8777 (tt0) cc_final: 0.8540 (tt0) outliers start: 43 outliers final: 33 residues processed: 297 average time/residue: 0.1600 time to fit residues: 68.0749 Evaluate side-chains 305 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 22 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 125 GLN I 125 GLN J 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.123105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.099179 restraints weight = 21154.475| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.83 r_work: 0.2903 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17697 Z= 0.148 Angle : 0.517 9.668 24039 Z= 0.264 Chirality : 0.043 0.176 2637 Planarity : 0.004 0.046 3066 Dihedral : 6.214 53.789 2793 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.51 % Allowed : 12.53 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2130 helix: 2.87 (0.26), residues: 354 sheet: -0.15 (0.23), residues: 477 loop : -0.79 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 75 TYR 0.015 0.001 TYR H 33 PHE 0.012 0.001 PHE a 9 TRP 0.010 0.001 TRP a 92 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00349 (17655) covalent geometry : angle 0.50754 (23934) SS BOND : bond 0.00324 ( 21) SS BOND : angle 0.61295 ( 42) hydrogen bonds : bond 0.03577 ( 683) hydrogen bonds : angle 5.11378 ( 1881) link_BETA1-4 : bond 0.00396 ( 6) link_BETA1-4 : angle 1.05693 ( 18) link_NAG-ASN : bond 0.00562 ( 15) link_NAG-ASN : angle 2.22228 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8322 (mmp80) cc_final: 0.8114 (mmp-170) REVERT: A 174 GLU cc_start: 0.8179 (mp0) cc_final: 0.7413 (mm-30) REVERT: A 258 TYR cc_start: 0.8962 (m-80) cc_final: 0.8740 (m-80) REVERT: a 17 MET cc_start: 0.9046 (ttm) cc_final: 0.8788 (ttm) REVERT: a 57 ASP cc_start: 0.8363 (m-30) cc_final: 0.8027 (m-30) REVERT: a 77 ILE cc_start: 0.9225 (mm) cc_final: 0.8946 (mm) REVERT: a 102 MET cc_start: 0.8746 (mtt) cc_final: 0.8444 (mtm) REVERT: B 63 ASP cc_start: 0.7848 (p0) cc_final: 0.7443 (t0) REVERT: I 17 MET cc_start: 0.9056 (ttm) cc_final: 0.8816 (ttm) REVERT: I 57 ASP cc_start: 0.8389 (m-30) cc_final: 0.7986 (m-30) REVERT: I 77 ILE cc_start: 0.9124 (mm) cc_final: 0.8885 (mm) REVERT: I 102 MET cc_start: 0.8718 (mtt) cc_final: 0.8484 (mtm) REVERT: I 161 GLN cc_start: 0.8792 (tt0) cc_final: 0.8497 (tt0) REVERT: C 14 CYS cc_start: 0.8835 (m) cc_final: 0.8431 (m) REVERT: E 3 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8421 (pp30) REVERT: E 38 ARG cc_start: 0.8955 (ptt-90) cc_final: 0.8709 (ptt180) REVERT: J 137 CYS cc_start: 0.8804 (m) cc_final: 0.8111 (m) REVERT: J 161 GLN cc_start: 0.8757 (tt0) cc_final: 0.8529 (tt0) outliers start: 28 outliers final: 26 residues processed: 300 average time/residue: 0.1665 time to fit residues: 70.8336 Evaluate side-chains 309 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 22 TYR Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN a 125 GLN I 125 GLN G 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095252 restraints weight = 21392.074| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.83 r_work: 0.2833 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17697 Z= 0.281 Angle : 0.606 10.562 24039 Z= 0.308 Chirality : 0.046 0.164 2637 Planarity : 0.004 0.046 3066 Dihedral : 6.459 54.789 2793 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.94 % Allowed : 12.80 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2130 helix: 2.60 (0.26), residues: 354 sheet: -0.21 (0.24), residues: 477 loop : -0.86 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 75 TYR 0.021 0.002 TYR E 33 PHE 0.015 0.002 PHE a 9 TRP 0.011 0.002 TRP a 92 HIS 0.007 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00673 (17655) covalent geometry : angle 0.59608 (23934) SS BOND : bond 0.00495 ( 21) SS BOND : angle 0.71779 ( 42) hydrogen bonds : bond 0.04065 ( 683) hydrogen bonds : angle 5.52285 ( 1881) link_BETA1-4 : bond 0.00239 ( 6) link_BETA1-4 : angle 1.23148 ( 18) link_NAG-ASN : bond 0.00532 ( 15) link_NAG-ASN : angle 2.49678 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8314 (mmp80) cc_final: 0.8101 (mmp-170) REVERT: A 174 GLU cc_start: 0.8163 (mp0) cc_final: 0.7444 (mm-30) REVERT: A 258 TYR cc_start: 0.9006 (m-80) cc_final: 0.8726 (m-80) REVERT: L 6 GLN cc_start: 0.8075 (tt0) cc_final: 0.7784 (tt0) REVERT: a 17 MET cc_start: 0.9122 (ttm) cc_final: 0.8869 (ttm) REVERT: a 57 ASP cc_start: 0.8399 (m-30) cc_final: 0.8023 (m-30) REVERT: a 77 ILE cc_start: 0.9267 (mm) cc_final: 0.9044 (mm) REVERT: a 102 MET cc_start: 0.8794 (mtt) cc_final: 0.8489 (mtm) REVERT: B 63 ASP cc_start: 0.7820 (p0) cc_final: 0.7439 (t0) REVERT: I 17 MET cc_start: 0.9132 (ttm) cc_final: 0.8860 (ttm) REVERT: I 57 ASP cc_start: 0.8393 (m-30) cc_final: 0.7979 (m-30) REVERT: I 77 ILE cc_start: 0.9216 (mm) cc_final: 0.8939 (mm) REVERT: I 102 MET cc_start: 0.8779 (mtt) cc_final: 0.8527 (mtm) REVERT: C 14 CYS cc_start: 0.8882 (m) cc_final: 0.8474 (m) REVERT: E 3 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8466 (pp30) REVERT: J 137 CYS cc_start: 0.8783 (m) cc_final: 0.8141 (m) REVERT: J 161 GLN cc_start: 0.8795 (tt0) cc_final: 0.8553 (tt0) outliers start: 36 outliers final: 31 residues processed: 288 average time/residue: 0.1646 time to fit residues: 67.3682 Evaluate side-chains 303 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 22 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 141 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 0.0060 chunk 119 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 125 GLN I 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100761 restraints weight = 20837.087| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.77 r_work: 0.2946 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17697 Z= 0.120 Angle : 0.511 10.349 24039 Z= 0.262 Chirality : 0.042 0.175 2637 Planarity : 0.004 0.046 3066 Dihedral : 6.228 53.524 2793 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.40 % Allowed : 13.39 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2130 helix: 2.91 (0.26), residues: 354 sheet: -0.11 (0.24), residues: 477 loop : -0.74 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 64 TYR 0.014 0.001 TYR E 33 PHE 0.012 0.001 PHE I 9 TRP 0.011 0.001 TRP G 35 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00276 (17655) covalent geometry : angle 0.50148 (23934) SS BOND : bond 0.00263 ( 21) SS BOND : angle 0.58765 ( 42) hydrogen bonds : bond 0.03401 ( 683) hydrogen bonds : angle 5.34747 ( 1881) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 0.93139 ( 18) link_NAG-ASN : bond 0.00617 ( 15) link_NAG-ASN : angle 2.22828 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8190 (mp0) cc_final: 0.7421 (mm-30) REVERT: A 258 TYR cc_start: 0.8935 (m-80) cc_final: 0.8722 (m-80) REVERT: a 17 MET cc_start: 0.9001 (ttm) cc_final: 0.8751 (ttm) REVERT: a 57 ASP cc_start: 0.8354 (m-30) cc_final: 0.8020 (m-30) REVERT: a 77 ILE cc_start: 0.9248 (mm) cc_final: 0.9000 (mm) REVERT: a 102 MET cc_start: 0.8734 (mtt) cc_final: 0.8436 (mtm) REVERT: B 63 ASP cc_start: 0.7890 (p0) cc_final: 0.7456 (t0) REVERT: I 17 MET cc_start: 0.9029 (ttm) cc_final: 0.8792 (ttm) REVERT: I 57 ASP cc_start: 0.8386 (m-30) cc_final: 0.7963 (m-30) REVERT: I 102 MET cc_start: 0.8680 (mtt) cc_final: 0.8443 (mtm) REVERT: I 161 GLN cc_start: 0.8797 (tt0) cc_final: 0.8505 (tt0) REVERT: C 14 CYS cc_start: 0.8768 (m) cc_final: 0.8418 (m) REVERT: C 174 GLU cc_start: 0.7978 (mp0) cc_final: 0.7350 (mm-30) REVERT: E 3 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8484 (pp30) REVERT: E 38 ARG cc_start: 0.8930 (ptt-90) cc_final: 0.8704 (ptt180) REVERT: J 137 CYS cc_start: 0.8789 (m) cc_final: 0.8133 (m) REVERT: J 161 GLN cc_start: 0.8758 (tt0) cc_final: 0.8531 (tt0) outliers start: 26 outliers final: 20 residues processed: 298 average time/residue: 0.1590 time to fit residues: 67.8439 Evaluate side-chains 290 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 73 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 22 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 78 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 125 GLN I 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097579 restraints weight = 21127.942| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.74 r_work: 0.2903 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17697 Z= 0.195 Angle : 0.562 11.068 24039 Z= 0.284 Chirality : 0.044 0.171 2637 Planarity : 0.004 0.046 3066 Dihedral : 6.366 54.187 2793 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.40 % Allowed : 13.55 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2130 helix: 2.73 (0.26), residues: 354 sheet: -0.07 (0.24), residues: 477 loop : -0.76 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 75 TYR 0.018 0.001 TYR E 33 PHE 0.013 0.002 PHE a 9 TRP 0.009 0.001 TRP G 35 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00467 (17655) covalent geometry : angle 0.54518 (23934) SS BOND : bond 0.00399 ( 21) SS BOND : angle 0.64476 ( 42) hydrogen bonds : bond 0.03669 ( 683) hydrogen bonds : angle 5.38960 ( 1881) link_BETA1-4 : bond 0.00422 ( 6) link_BETA1-4 : angle 1.18177 ( 18) link_NAG-ASN : bond 0.00531 ( 15) link_NAG-ASN : angle 3.09310 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5308.84 seconds wall clock time: 91 minutes 33.89 seconds (5493.89 seconds total)