Starting phenix.real_space_refine on Thu Mar 5 01:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o8q_70233/03_2026/9o8q_70233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o8q_70233/03_2026/9o8q_70233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o8q_70233/03_2026/9o8q_70233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o8q_70233/03_2026/9o8q_70233.map" model { file = "/net/cci-nas-00/data/ceres_data/9o8q_70233/03_2026/9o8q_70233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o8q_70233/03_2026/9o8q_70233.cif" } resolution = 2.62 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= -0.000 sd= 0.010 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 81 5.16 5 C 10914 2.51 5 N 2991 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17502 Number of models: 1 Model: "" Number of chains: 30 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2471 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1388 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2471 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1388 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "I" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2471 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "F" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1388 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.45, per 1000 atoms: 0.25 Number of scatterers: 17502 At special positions: 0 Unit cell: (129.958, 119.188, 145.036, 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 81 16.00 O 3516 8.00 N 2991 7.00 C 10914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.02 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.02 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.02 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.02 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 133 " " NAG A 403 " - " ASN A 158 " " NAG A 404 " - " ASN A 246 " " NAG A 405 " - " ASN A 126 " " NAG A 406 " - " ASN A 45 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 133 " " NAG C 403 " - " ASN C 158 " " NAG C 404 " - " ASN C 246 " " NAG C 405 " - " ASN C 126 " " NAG C 406 " - " ASN C 45 " " NAG D 401 " - " ASN D 22 " " NAG D 402 " - " ASN D 133 " " NAG D 403 " - " ASN D 158 " " NAG D 404 " - " ASN D 246 " " NAG D 405 " - " ASN D 126 " " NAG D 406 " - " ASN D 45 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 63 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN A 165 " " NAG Q 1 " - " ASN C 38 " " NAG R 1 " - " ASN C 63 " " NAG S 1 " - " ASN C 285 " " NAG T 1 " - " ASN C 165 " " NAG U 1 " - " ASN D 38 " " NAG V 1 " - " ASN D 63 " " NAG W 1 " - " ASN D 285 " " NAG X 1 " - " ASN D 165 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 838.8 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 51 sheets defined 19.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.573A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.813A pdb=" N ILE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.379A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.574A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 37 through 53 Processing helix chain 'E' and resid 75 through 126 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.813A pdb=" N ILE E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 171 removed outlier: 4.379A pdb=" N TYR E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.571A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.505A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 53 Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.811A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.377A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP F 164 " --> pdb=" O ASN F 160 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU F 165 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.713A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.858A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.780A pdb=" N PHE H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY H 96 " --> pdb=" O PHE H 100D" (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE H 100D" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.724A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.398A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.610A pdb=" N PHE B 24 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.042A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60 removed outlier: 7.356A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.102A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 257 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100 through 101 removed outlier: 8.023A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.764A pdb=" N ALA A 138 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N SER A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AB8, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AB9, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.714A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.859A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.776A pdb=" N PHE G 102 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY G 96 " --> pdb=" O PHE G 100D" (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE G 100D" --> pdb=" O GLY G 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.732A pdb=" N VAL J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.399A pdb=" N TRP J 35 " --> pdb=" O MET J 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL J 97 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 36 removed outlier: 3.611A pdb=" N PHE E 24 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.046A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 58 through 60 removed outlier: 7.357A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.105A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 257 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 101 removed outlier: 8.025A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.764A pdb=" N ALA C 138 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N SER C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AD7, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AD8, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.714A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 80 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.852A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.776A pdb=" N PHE I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY I 96 " --> pdb=" O PHE I 100D" (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE I 100D" --> pdb=" O GLY I 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AE3, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.725A pdb=" N VAL K 11 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.398A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL K 97 " --> pdb=" O SER K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.614A pdb=" N PHE F 24 " --> pdb=" O ALA F 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AE7, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=AE8, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AE9, first strand: chain 'D' and resid 51 through 52 removed outlier: 6.047A pdb=" N ILE D 51 " --> pdb=" O GLY D 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 58 through 60 removed outlier: 7.347A pdb=" N LEU D 59 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 100 through 101 removed outlier: 5.097A pdb=" N ILE D 179 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY D 256 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 257 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 100 through 101 removed outlier: 8.024A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 136 through 141 removed outlier: 7.758A pdb=" N ALA D 138 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N SER D 144 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 167 through 169 Processing sheet with id=AF6, first strand: chain 'D' and resid 303 through 304 665 hydrogen bonds defined for protein. 1734 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: 3.70 Time building geometry restraints manager: 2.31 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: 5637 1.34 - 1.46: 4515 1.46 - 1.59: 7608 1.59 - 1.71: 0 1.71 - 1.83: 111 Bond restraints: 17871 Sorted by residual: bond pdb=" C1 BMA T 3 " pdb=" O5 BMA T 3 " ideal model delta sigma weight residual 1.410 1.508 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sigma weight residual 1.410 1.507 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C1 BMA X 3 " pdb=" O5 BMA X 3 " ideal model delta sigma weight residual 1.410 1.507 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C5 BMA X 3 " pdb=" O5 BMA X 3 " ideal model delta sigma weight residual 1.417 1.478 -0.061 2.00e-02 2.50e+03 9.23e+00 bond pdb=" C5 BMA T 3 " pdb=" O5 BMA T 3 " ideal model delta sigma weight residual 1.417 1.477 -0.060 2.00e-02 2.50e+03 9.12e+00 ... (remaining 17866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 22258 1.53 - 3.06: 1576 3.06 - 4.59: 245 4.59 - 6.12: 92 6.12 - 7.65: 24 Bond angle restraints: 24195 Sorted by residual: angle pdb=" N GLY C 263 " pdb=" CA GLY C 263 " pdb=" C GLY C 263 " ideal model delta sigma weight residual 110.71 117.09 -6.38 1.53e+00 4.27e-01 1.74e+01 angle pdb=" N GLY A 263 " pdb=" CA GLY A 263 " pdb=" C GLY A 263 " ideal model delta sigma weight residual 110.71 117.06 -6.35 1.53e+00 4.27e-01 1.72e+01 angle pdb=" N GLY D 263 " pdb=" CA GLY D 263 " pdb=" C GLY D 263 " ideal model delta sigma weight residual 110.71 117.05 -6.34 1.53e+00 4.27e-01 1.72e+01 angle pdb=" N PHE C 148 " pdb=" CA PHE C 148 " pdb=" CB PHE C 148 " ideal model delta sigma weight residual 109.83 116.02 -6.19 1.51e+00 4.39e-01 1.68e+01 angle pdb=" N PHE A 148 " pdb=" CA PHE A 148 " pdb=" CB PHE A 148 " ideal model delta sigma weight residual 109.83 116.00 -6.17 1.51e+00 4.39e-01 1.67e+01 ... (remaining 24190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.86: 10182 22.86 - 45.72: 834 45.72 - 68.58: 219 68.58 - 91.44: 78 91.44 - 114.30: 33 Dihedral angle restraints: 11346 sinusoidal: 5223 harmonic: 6123 Sorted by residual: dihedral pdb=" CD ARG D 229 " pdb=" NE ARG D 229 " pdb=" CZ ARG D 229 " pdb=" NH1 ARG D 229 " ideal model delta sinusoidal sigma weight residual 0.00 -70.95 70.95 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CD ARG A 229 " pdb=" NE ARG A 229 " pdb=" CZ ARG A 229 " pdb=" NH1 ARG A 229 " ideal model delta sinusoidal sigma weight residual 0.00 -70.89 70.89 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CD ARG C 229 " pdb=" NE ARG C 229 " pdb=" CZ ARG C 229 " pdb=" NH1 ARG C 229 " ideal model delta sinusoidal sigma weight residual 0.00 -70.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 11343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2623 0.116 - 0.231: 134 0.231 - 0.347: 12 0.347 - 0.462: 0 0.462 - 0.578: 3 Chirality restraints: 2772 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.30e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN D 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.28e+00 ... (remaining 2769 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 229 " 0.921 9.50e-02 1.11e+02 4.13e-01 1.09e+02 pdb=" NE ARG A 229 " -0.071 2.00e-02 2.50e+03 pdb=" CZ ARG A 229 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 229 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 229 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 229 " 0.921 9.50e-02 1.11e+02 4.13e-01 1.09e+02 pdb=" NE ARG C 229 " -0.071 2.00e-02 2.50e+03 pdb=" CZ ARG C 229 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG C 229 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 229 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 229 " 0.920 9.50e-02 1.11e+02 4.13e-01 1.09e+02 pdb=" NE ARG D 229 " -0.071 2.00e-02 2.50e+03 pdb=" CZ ARG D 229 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG D 229 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 229 " 0.007 2.00e-02 2.50e+03 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 496 2.68 - 3.23: 16448 3.23 - 3.79: 27785 3.79 - 4.34: 39411 4.34 - 4.90: 64314 Nonbonded interactions: 148454 Sorted by model distance: nonbonded pdb=" OD2 ASP B 79 " pdb=" OG SER D 110 " model vdw 2.124 3.040 nonbonded pdb=" OG SER A 110 " pdb=" OD2 ASP E 79 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 110 " pdb=" OD2 ASP F 79 " model vdw 2.137 3.040 nonbonded pdb=" O SER G 62 " pdb=" NH2 ARG G 66 " model vdw 2.210 3.120 nonbonded pdb=" O SER I 62 " pdb=" NH2 ARG I 66 " model vdw 2.210 3.120 ... (remaining 148449 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) } 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: 8.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.350 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.006 0.098 17952 Z= 0.272 Angle : 0.946 10.112 24414 Z= 0.472 Chirality : 0.059 0.578 2772 Planarity : 0.022 0.413 3069 Dihedral : 19.156 114.303 7380 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.82 % Allowed : 20.26 % Favored : 78.91 % 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: -1.75 (0.17), residues: 2124 helix: 0.06 (0.26), residues: 351 sheet: -1.90 (0.21), residues: 507 loop : -1.16 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.005 ARG D 150 TYR 0.023 0.002 TYR D 98 PHE 0.040 0.004 PHE B 9 TRP 0.007 0.001 TRP G 98 HIS 0.008 0.002 HIS D 17 Details of bonding type rmsd covalent geometry : bond 0.00602 (17871) covalent geometry : angle 0.90530 (24195) SS BOND : bond 0.00615 ( 24) SS BOND : angle 1.31182 ( 48) hydrogen bonds : bond 0.19649 ( 614) hydrogen bonds : angle 8.76351 ( 1734) link_BETA1-4 : bond 0.01265 ( 21) link_BETA1-4 : angle 3.78054 ( 63) link_BETA1-6 : bond 0.00364 ( 3) link_BETA1-6 : angle 1.33716 ( 9) link_NAG-ASN : bond 0.00557 ( 33) link_NAG-ASN : angle 3.19275 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 424 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7059 (mt0) cc_final: 0.6677 (mt0) REVERT: H 64 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8241 (tttm) REVERT: L 31 HIS cc_start: 0.7414 (p-80) cc_final: 0.6881 (p-80) REVERT: L 50 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: L 79 GLN cc_start: 0.8179 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 35 GLU cc_start: 0.8536 (tt0) cc_final: 0.8320 (tt0) REVERT: A 77 ASP cc_start: 0.7545 (m-30) cc_final: 0.7198 (OUTLIER) REVERT: A 83 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7823 (mtmm) REVERT: A 165 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7094 (t0) REVERT: A 187 THR cc_start: 0.7729 (m) cc_final: 0.7395 (p) REVERT: A 198 SER cc_start: 0.8676 (m) cc_final: 0.8426 (p) REVERT: G 1 GLN cc_start: 0.6989 (mt0) cc_final: 0.6613 (mt0) REVERT: J 31 HIS cc_start: 0.7487 (p-80) cc_final: 0.6834 (p-80) REVERT: J 79 GLN cc_start: 0.8190 (tt0) cc_final: 0.7830 (tm-30) REVERT: C 35 GLU cc_start: 0.8554 (tt0) cc_final: 0.8334 (tt0) REVERT: C 77 ASP cc_start: 0.7539 (m-30) cc_final: 0.7199 (OUTLIER) REVERT: C 83 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8162 (mtpm) REVERT: C 165 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6987 (t0) REVERT: C 187 THR cc_start: 0.7686 (m) cc_final: 0.7354 (p) REVERT: C 198 SER cc_start: 0.8629 (m) cc_final: 0.8393 (p) REVERT: E 76 ARG cc_start: 0.7647 (ttt-90) cc_final: 0.7381 (ttt-90) REVERT: I 1 GLN cc_start: 0.6980 (mt0) cc_final: 0.6648 (mt0) REVERT: K 31 HIS cc_start: 0.7453 (p-80) cc_final: 0.6813 (p-80) REVERT: K 50 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: K 79 GLN cc_start: 0.8101 (tt0) cc_final: 0.7851 (tm-30) REVERT: D 33 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7005 (mtp85) REVERT: D 77 ASP cc_start: 0.7550 (m-30) cc_final: 0.7292 (OUTLIER) REVERT: D 83 LYS cc_start: 0.8418 (mtpp) cc_final: 0.7747 (mtmm) REVERT: D 165 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7121 (t0) REVERT: D 187 THR cc_start: 0.7723 (m) cc_final: 0.7353 (p) REVERT: D 197 GLN cc_start: 0.8095 (pt0) cc_final: 0.7826 (pt0) REVERT: D 198 SER cc_start: 0.8698 (m) cc_final: 0.8425 (p) REVERT: D 220 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7885 (ttm110) REVERT: F 74 GLU cc_start: 0.6394 (tt0) cc_final: 0.5680 (mt-10) REVERT: F 120 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7755 (mm-30) outliers start: 15 outliers final: 7 residues processed: 437 average time/residue: 0.6344 time to fit residues: 309.3626 Evaluate side-chains 297 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 288 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 HIS A 17 HIS A 18 HIS A 56 HIS B 60 ASN B 125 GLN B 159 HIS J 39 HIS C 18 HIS C 56 HIS E 28 ASN E 60 ASN E 125 GLN E 159 HIS K 39 HIS D 17 HIS D 56 HIS D 171 ASN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 60 ASN F 159 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118276 restraints weight = 30948.427| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.74 r_work: 0.3536 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 17952 Z= 0.232 Angle : 0.732 10.836 24414 Z= 0.372 Chirality : 0.050 0.257 2772 Planarity : 0.005 0.056 3069 Dihedral : 11.576 86.494 3527 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.56 % Allowed : 23.12 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.28 (0.17), residues: 2124 helix: 0.62 (0.26), residues: 348 sheet: -1.45 (0.22), residues: 501 loop : -0.99 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 76 TYR 0.015 0.002 TYR C 195 PHE 0.040 0.003 PHE A 147 TRP 0.013 0.001 TRP C 153 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00538 (17871) covalent geometry : angle 0.70768 (24195) SS BOND : bond 0.00490 ( 24) SS BOND : angle 1.74950 ( 48) hydrogen bonds : bond 0.04962 ( 614) hydrogen bonds : angle 6.50304 ( 1734) link_BETA1-4 : bond 0.00726 ( 21) link_BETA1-4 : angle 2.51148 ( 63) link_BETA1-6 : bond 0.00098 ( 3) link_BETA1-6 : angle 1.24284 ( 9) link_NAG-ASN : bond 0.00513 ( 33) link_NAG-ASN : angle 2.03883 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 300 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7503 (mt0) cc_final: 0.7060 (mt0) REVERT: H 105 GLN cc_start: 0.7485 (pp30) cc_final: 0.7284 (pp30) REVERT: L 31 HIS cc_start: 0.7735 (p-80) cc_final: 0.7385 (p-80) REVERT: L 79 GLN cc_start: 0.8091 (tt0) cc_final: 0.7744 (tm-30) REVERT: A 50 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: A 77 ASP cc_start: 0.7872 (m-30) cc_final: 0.7174 (OUTLIER) REVERT: A 197 GLN cc_start: 0.8073 (pt0) cc_final: 0.7835 (pt0) REVERT: A 198 SER cc_start: 0.8740 (m) cc_final: 0.8499 (p) REVERT: G 1 GLN cc_start: 0.7383 (mt0) cc_final: 0.6980 (mt0) REVERT: G 105 GLN cc_start: 0.7527 (pp30) cc_final: 0.7325 (pp30) REVERT: J 31 HIS cc_start: 0.7894 (p-80) cc_final: 0.7486 (p-80) REVERT: C 33 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7489 (mtp85) REVERT: C 77 ASP cc_start: 0.7780 (m-30) cc_final: 0.7237 (OUTLIER) REVERT: C 241 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8146 (t0) REVERT: I 1 GLN cc_start: 0.7393 (mt0) cc_final: 0.6942 (mt0) REVERT: K 31 HIS cc_start: 0.7769 (p-80) cc_final: 0.7266 (p-80) REVERT: K 61 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6101 (mtm110) REVERT: K 79 GLN cc_start: 0.8214 (tt0) cc_final: 0.7840 (tm-30) REVERT: D 77 ASP cc_start: 0.7755 (m-30) cc_final: 0.7270 (OUTLIER) REVERT: D 168 MET cc_start: 0.7675 (tpp) cc_final: 0.7367 (mmm) REVERT: D 198 SER cc_start: 0.8795 (m) cc_final: 0.8547 (p) REVERT: F 74 GLU cc_start: 0.6800 (tt0) cc_final: 0.6064 (mt-10) REVERT: F 133 MET cc_start: 0.7789 (mtp) cc_final: 0.7565 (mtm) outliers start: 83 outliers final: 40 residues processed: 356 average time/residue: 0.5628 time to fit residues: 225.2203 Evaluate side-chains 298 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 190 optimal weight: 0.2980 chunk 146 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 81 ASN B 60 ASN J 79 GLN C 18 HIS C 81 ASN C 210 GLN E 60 ASN D 18 HIS D 81 ASN D 171 ASN F 28 ASN F 60 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114724 restraints weight = 31470.387| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.81 r_work: 0.3465 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17952 Z= 0.143 Angle : 0.652 9.531 24414 Z= 0.321 Chirality : 0.048 0.314 2772 Planarity : 0.004 0.055 3069 Dihedral : 9.177 76.696 3510 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.08 % Allowed : 25.15 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.97 (0.17), residues: 2124 helix: 0.98 (0.26), residues: 351 sheet: -1.20 (0.22), residues: 513 loop : -0.83 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.014 0.001 TYR I 79 PHE 0.034 0.002 PHE A 147 TRP 0.009 0.001 TRP J 35 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00322 (17871) covalent geometry : angle 0.62852 (24195) SS BOND : bond 0.00330 ( 24) SS BOND : angle 1.73573 ( 48) hydrogen bonds : bond 0.04457 ( 614) hydrogen bonds : angle 6.01511 ( 1734) link_BETA1-4 : bond 0.00759 ( 21) link_BETA1-4 : angle 2.47616 ( 63) link_BETA1-6 : bond 0.00170 ( 3) link_BETA1-6 : angle 1.27019 ( 9) link_NAG-ASN : bond 0.00451 ( 33) link_NAG-ASN : angle 1.70343 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 303 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7280 (mt0) cc_final: 0.6809 (mt0) REVERT: H 64 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8251 (tttm) REVERT: L 31 HIS cc_start: 0.7600 (p-80) cc_final: 0.7247 (p-80) REVERT: A 70 LEU cc_start: 0.7847 (mt) cc_final: 0.7465 (tp) REVERT: A 77 ASP cc_start: 0.7535 (m-30) cc_final: 0.6905 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: A 198 SER cc_start: 0.8644 (m) cc_final: 0.8368 (p) REVERT: G 1 GLN cc_start: 0.7262 (mt0) cc_final: 0.6847 (mt0) REVERT: G 82 MET cc_start: 0.8182 (mtm) cc_final: 0.7796 (mtt) REVERT: G 105 GLN cc_start: 0.7305 (pp30) cc_final: 0.7057 (pp30) REVERT: J 31 HIS cc_start: 0.7709 (p-80) cc_final: 0.7157 (p-80) REVERT: C 33 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7284 (mtp85) REVERT: C 77 ASP cc_start: 0.7536 (m-30) cc_final: 0.7033 (OUTLIER) REVERT: C 213 VAL cc_start: 0.8585 (t) cc_final: 0.8340 (m) REVERT: E 10 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7452 (mp) REVERT: E 76 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7426 (ttt-90) REVERT: I 1 GLN cc_start: 0.7225 (mt0) cc_final: 0.6749 (mt0) REVERT: I 105 GLN cc_start: 0.7552 (pp30) cc_final: 0.7235 (pp30) REVERT: K 31 HIS cc_start: 0.7688 (p-80) cc_final: 0.7156 (p-80) REVERT: K 42 LYS cc_start: 0.6154 (mtmm) cc_final: 0.5913 (mtmm) REVERT: D 33 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7735 (ttm110) REVERT: D 70 LEU cc_start: 0.8020 (mt) cc_final: 0.7629 (tp) REVERT: D 77 ASP cc_start: 0.7571 (m-30) cc_final: 0.7157 (OUTLIER) REVERT: F 19 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7490 (t0) REVERT: F 74 GLU cc_start: 0.6659 (tt0) cc_final: 0.5778 (mt-10) REVERT: F 145 ASP cc_start: 0.8246 (p0) cc_final: 0.7918 (p0) outliers start: 56 outliers final: 25 residues processed: 337 average time/residue: 0.5726 time to fit residues: 217.0001 Evaluate side-chains 301 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain F residue 19 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 207 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 164 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 195 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN A 18 HIS B 60 ASN J 79 GLN C 18 HIS E 60 ASN K 69 ASN K 79 GLN D 18 HIS D 171 ASN F 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112748 restraints weight = 31259.844| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.81 r_work: 0.3426 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17952 Z= 0.186 Angle : 0.687 11.098 24414 Z= 0.341 Chirality : 0.048 0.301 2772 Planarity : 0.004 0.055 3069 Dihedral : 8.064 67.917 3510 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.56 % Allowed : 24.77 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.83 (0.17), residues: 2124 helix: 1.10 (0.26), residues: 354 sheet: -0.98 (0.22), residues: 507 loop : -0.82 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 76 TYR 0.015 0.002 TYR G 79 PHE 0.038 0.002 PHE D 147 TRP 0.007 0.001 TRP C 234 HIS 0.006 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00424 (17871) covalent geometry : angle 0.65691 (24195) SS BOND : bond 0.00690 ( 24) SS BOND : angle 2.92444 ( 48) hydrogen bonds : bond 0.04465 ( 614) hydrogen bonds : angle 5.87490 ( 1734) link_BETA1-4 : bond 0.00599 ( 21) link_BETA1-4 : angle 2.41139 ( 63) link_BETA1-6 : bond 0.00125 ( 3) link_BETA1-6 : angle 1.24119 ( 9) link_NAG-ASN : bond 0.00415 ( 33) link_NAG-ASN : angle 1.74766 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 287 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7373 (mt0) cc_final: 0.6892 (mt0) REVERT: H 64 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8277 (tttm) REVERT: H 105 GLN cc_start: 0.7362 (pp30) cc_final: 0.7085 (pp30) REVERT: L 31 HIS cc_start: 0.7617 (p-80) cc_final: 0.7221 (p-80) REVERT: A 33 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7250 (mtp85) REVERT: A 70 LEU cc_start: 0.7843 (mt) cc_final: 0.7511 (tp) REVERT: A 77 ASP cc_start: 0.7557 (m-30) cc_final: 0.7003 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: A 198 SER cc_start: 0.8669 (m) cc_final: 0.8386 (p) REVERT: G 1 GLN cc_start: 0.7282 (mt0) cc_final: 0.6829 (mt0) REVERT: G 20 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7452 (mt) REVERT: G 64 LYS cc_start: 0.8705 (tttm) cc_final: 0.8496 (ttpp) REVERT: G 81 GLN cc_start: 0.6797 (tp-100) cc_final: 0.6590 (tp40) REVERT: G 82 MET cc_start: 0.8286 (mtm) cc_final: 0.7853 (mtt) REVERT: G 107 THR cc_start: 0.5620 (OUTLIER) cc_final: 0.5286 (t) REVERT: J 31 HIS cc_start: 0.7750 (p-80) cc_final: 0.7296 (p-80) REVERT: J 47 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: C 33 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7280 (mtp85) REVERT: C 77 ASP cc_start: 0.7539 (m-30) cc_final: 0.7096 (OUTLIER) REVERT: E 76 ARG cc_start: 0.7904 (ttt-90) cc_final: 0.7465 (ttt-90) REVERT: I 82 MET cc_start: 0.8299 (mtt) cc_final: 0.8068 (mtt) REVERT: K 31 HIS cc_start: 0.7755 (p-80) cc_final: 0.7465 (p-80) REVERT: K 61 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6131 (mtm110) REVERT: D 33 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7177 (mtp85) REVERT: D 62 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: D 70 LEU cc_start: 0.7985 (mt) cc_final: 0.7653 (tp) REVERT: D 77 ASP cc_start: 0.7639 (m-30) cc_final: 0.7228 (OUTLIER) REVERT: D 244 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (tt) REVERT: F 74 GLU cc_start: 0.6718 (tt0) cc_final: 0.5818 (mt-10) outliers start: 83 outliers final: 43 residues processed: 339 average time/residue: 0.6017 time to fit residues: 228.0248 Evaluate side-chains 310 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 191 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 18 HIS E 60 ASN D 18 HIS D 171 ASN F 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112142 restraints weight = 31013.087| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.75 r_work: 0.3423 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17952 Z= 0.185 Angle : 0.676 10.375 24414 Z= 0.334 Chirality : 0.047 0.325 2772 Planarity : 0.004 0.051 3069 Dihedral : 7.330 57.429 3510 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.78 % Allowed : 24.88 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.17), residues: 2124 helix: 1.24 (0.26), residues: 348 sheet: -0.85 (0.22), residues: 507 loop : -0.78 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 76 TYR 0.013 0.002 TYR C 195 PHE 0.040 0.002 PHE A 147 TRP 0.009 0.001 TRP J 35 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00422 (17871) covalent geometry : angle 0.64844 (24195) SS BOND : bond 0.00804 ( 24) SS BOND : angle 2.48264 ( 48) hydrogen bonds : bond 0.04400 ( 614) hydrogen bonds : angle 5.78717 ( 1734) link_BETA1-4 : bond 0.00531 ( 21) link_BETA1-4 : angle 2.37103 ( 63) link_BETA1-6 : bond 0.00248 ( 3) link_BETA1-6 : angle 1.29885 ( 9) link_NAG-ASN : bond 0.00368 ( 33) link_NAG-ASN : angle 1.79255 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 270 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7456 (mt0) cc_final: 0.6966 (mt0) REVERT: H 68 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7917 (m) REVERT: H 105 GLN cc_start: 0.7411 (pp30) cc_final: 0.7204 (pp30) REVERT: L 31 HIS cc_start: 0.7801 (p-80) cc_final: 0.7407 (p-80) REVERT: A 33 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7290 (mtp85) REVERT: A 77 ASP cc_start: 0.7704 (m-30) cc_final: 0.7107 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: B 6 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7133 (mp) REVERT: G 64 LYS cc_start: 0.8716 (tttm) cc_final: 0.8500 (ttpp) REVERT: G 82 MET cc_start: 0.8306 (mtm) cc_final: 0.7930 (mtt) REVERT: G 105 GLN cc_start: 0.7394 (pp30) cc_final: 0.7138 (pp30) REVERT: J 31 HIS cc_start: 0.8002 (p-80) cc_final: 0.7434 (p-80) REVERT: J 47 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: C 33 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7314 (mtp85) REVERT: C 77 ASP cc_start: 0.7700 (m-30) cc_final: 0.7189 (OUTLIER) REVERT: C 201 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6860 (mtm-85) REVERT: C 246 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8740 (t0) REVERT: E 72 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: E 76 ARG cc_start: 0.7938 (ttt-90) cc_final: 0.7461 (ttt-90) REVERT: I 1 GLN cc_start: 0.7475 (mt0) cc_final: 0.6983 (mt0) REVERT: I 82 MET cc_start: 0.8336 (mtt) cc_final: 0.8105 (mtt) REVERT: I 105 GLN cc_start: 0.7340 (pp30) cc_final: 0.7042 (pp30) REVERT: K 31 HIS cc_start: 0.7951 (p-80) cc_final: 0.7596 (p-80) REVERT: K 61 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6203 (mtm110) REVERT: D 33 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7224 (mtp85) REVERT: D 62 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: D 77 ASP cc_start: 0.7793 (m-30) cc_final: 0.7340 (OUTLIER) REVERT: D 244 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8563 (tt) outliers start: 87 outliers final: 54 residues processed: 328 average time/residue: 0.6204 time to fit residues: 227.5786 Evaluate side-chains 312 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 18 HIS B 60 ASN G 81 GLN C 18 HIS E 60 ASN D 18 HIS D 171 ASN F 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.113073 restraints weight = 30884.659| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.77 r_work: 0.3430 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17952 Z= 0.163 Angle : 0.651 10.313 24414 Z= 0.321 Chirality : 0.047 0.349 2772 Planarity : 0.004 0.050 3069 Dihedral : 6.899 55.825 3510 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.17 % Allowed : 26.08 % Favored : 69.74 % 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: -0.70 (0.17), residues: 2124 helix: 1.27 (0.26), residues: 354 sheet: -0.75 (0.22), residues: 507 loop : -0.83 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 76 TYR 0.014 0.001 TYR I 79 PHE 0.041 0.002 PHE A 147 TRP 0.007 0.001 TRP J 35 HIS 0.004 0.001 HIS F 64 Details of bonding type rmsd covalent geometry : bond 0.00371 (17871) covalent geometry : angle 0.62605 (24195) SS BOND : bond 0.00351 ( 24) SS BOND : angle 2.16277 ( 48) hydrogen bonds : bond 0.04274 ( 614) hydrogen bonds : angle 5.67949 ( 1734) link_BETA1-4 : bond 0.00531 ( 21) link_BETA1-4 : angle 2.29810 ( 63) link_BETA1-6 : bond 0.00119 ( 3) link_BETA1-6 : angle 1.29270 ( 9) link_NAG-ASN : bond 0.00331 ( 33) link_NAG-ASN : angle 1.70331 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 268 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 64 LYS cc_start: 0.8732 (tttm) cc_final: 0.8505 (ttpp) REVERT: H 68 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7741 (m) REVERT: H 105 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7171 (pp30) REVERT: L 31 HIS cc_start: 0.7610 (p-80) cc_final: 0.7224 (p-80) REVERT: A 33 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7243 (mtp85) REVERT: A 70 LEU cc_start: 0.7975 (tp) cc_final: 0.7667 (tp) REVERT: A 77 ASP cc_start: 0.7552 (m-30) cc_final: 0.7024 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: G 1 GLN cc_start: 0.7376 (mt0) cc_final: 0.6605 (mt0) REVERT: G 64 LYS cc_start: 0.8710 (tttm) cc_final: 0.8501 (ttpp) REVERT: G 82 MET cc_start: 0.8376 (mtm) cc_final: 0.8031 (mtt) REVERT: G 105 GLN cc_start: 0.7404 (pp30) cc_final: 0.7119 (pp30) REVERT: J 31 HIS cc_start: 0.7756 (p-80) cc_final: 0.7182 (p-80) REVERT: J 47 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7737 (mmm) REVERT: C 33 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7257 (mtp85) REVERT: C 70 LEU cc_start: 0.7952 (tp) cc_final: 0.7637 (tp) REVERT: C 77 ASP cc_start: 0.7555 (m-30) cc_final: 0.7120 (OUTLIER) REVERT: C 201 ARG cc_start: 0.6942 (mtm180) cc_final: 0.6706 (mtm-85) REVERT: C 246 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8673 (t0) REVERT: E 39 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8271 (ttmm) REVERT: E 76 ARG cc_start: 0.7923 (ttt-90) cc_final: 0.7441 (ttt-90) REVERT: I 1 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6824 (mt0) REVERT: I 64 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8083 (tttt) REVERT: I 105 GLN cc_start: 0.7289 (pp30) cc_final: 0.7063 (pp30) REVERT: K 31 HIS cc_start: 0.7775 (p-80) cc_final: 0.7429 (p-80) REVERT: K 61 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6222 (mtm110) REVERT: D 33 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7188 (mtp85) REVERT: D 62 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: D 70 LEU cc_start: 0.8049 (tp) cc_final: 0.7686 (tp) REVERT: D 77 ASP cc_start: 0.7626 (m-30) cc_final: 0.7261 (OUTLIER) REVERT: D 83 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8602 (mtmm) REVERT: D 244 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8462 (tt) REVERT: F 74 GLU cc_start: 0.6581 (tt0) cc_final: 0.5701 (mt-10) outliers start: 76 outliers final: 42 residues processed: 313 average time/residue: 0.5738 time to fit residues: 201.5063 Evaluate side-chains 300 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 97 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN B 60 ASN G 81 GLN C 18 HIS E 60 ASN D 17 HIS D 18 HIS F 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111485 restraints weight = 31090.497| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.76 r_work: 0.3412 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17952 Z= 0.201 Angle : 0.671 11.080 24414 Z= 0.332 Chirality : 0.048 0.481 2772 Planarity : 0.004 0.050 3069 Dihedral : 6.718 56.030 3510 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.89 % Allowed : 25.70 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.76 (0.17), residues: 2124 helix: 1.11 (0.26), residues: 366 sheet: -0.88 (0.23), residues: 495 loop : -0.81 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 76 TYR 0.014 0.002 TYR C 195 PHE 0.042 0.002 PHE A 147 TRP 0.007 0.001 TRP C 234 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00460 (17871) covalent geometry : angle 0.64620 (24195) SS BOND : bond 0.00406 ( 24) SS BOND : angle 2.16450 ( 48) hydrogen bonds : bond 0.04421 ( 614) hydrogen bonds : angle 5.71001 ( 1734) link_BETA1-4 : bond 0.00565 ( 21) link_BETA1-4 : angle 2.19358 ( 63) link_BETA1-6 : bond 0.00215 ( 3) link_BETA1-6 : angle 1.29672 ( 9) link_NAG-ASN : bond 0.00366 ( 33) link_NAG-ASN : angle 1.83289 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 261 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 64 LYS cc_start: 0.8723 (tttm) cc_final: 0.8487 (ttpp) REVERT: H 68 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7798 (m) REVERT: H 81 GLN cc_start: 0.6863 (tp-100) cc_final: 0.6626 (tp40) REVERT: H 105 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7177 (pp30) REVERT: A 33 ARG cc_start: 0.8268 (mtt180) cc_final: 0.7239 (mtp85) REVERT: A 41 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8530 (tp30) REVERT: A 62 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: A 70 LEU cc_start: 0.8078 (tp) cc_final: 0.7800 (tp) REVERT: A 77 ASP cc_start: 0.7708 (m-30) cc_final: 0.7142 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: G 1 GLN cc_start: 0.7409 (mt0) cc_final: 0.6808 (mt0) REVERT: G 64 LYS cc_start: 0.8713 (tttm) cc_final: 0.8497 (ttpp) REVERT: G 82 MET cc_start: 0.8383 (mtm) cc_final: 0.8010 (mtt) REVERT: G 105 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: J 31 HIS cc_start: 0.8021 (p-80) cc_final: 0.7485 (p-80) REVERT: J 47 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7875 (mmm) REVERT: C 33 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7272 (mtp85) REVERT: C 70 LEU cc_start: 0.8116 (tp) cc_final: 0.7789 (tp) REVERT: C 77 ASP cc_start: 0.7685 (m-30) cc_final: 0.7231 (OUTLIER) REVERT: C 201 ARG cc_start: 0.7190 (mtm180) cc_final: 0.6979 (mtm-85) REVERT: C 220 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8272 (mtt90) REVERT: C 246 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8743 (t0) REVERT: E 76 ARG cc_start: 0.7948 (ttt-90) cc_final: 0.7441 (ttt-90) REVERT: E 143 LYS cc_start: 0.6681 (mttt) cc_final: 0.6353 (mttp) REVERT: I 1 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6923 (mt0) REVERT: I 68 THR cc_start: 0.7925 (t) cc_final: 0.7703 (m) REVERT: I 105 GLN cc_start: 0.7319 (pp30) cc_final: 0.7061 (pp30) REVERT: K 31 HIS cc_start: 0.7995 (p-80) cc_final: 0.7579 (p-80) REVERT: K 61 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6223 (mtm110) REVERT: D 33 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7225 (mtp85) REVERT: D 62 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: D 70 LEU cc_start: 0.8184 (tp) cc_final: 0.7834 (tp) REVERT: D 77 ASP cc_start: 0.7762 (m-30) cc_final: 0.7330 (OUTLIER) REVERT: D 201 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6847 (mtm-85) REVERT: D 244 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8565 (tt) REVERT: D 295 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: F 74 GLU cc_start: 0.6696 (tt0) cc_final: 0.5749 (mt-10) REVERT: F 133 MET cc_start: 0.7648 (mtp) cc_final: 0.7373 (mtm) outliers start: 89 outliers final: 55 residues processed: 317 average time/residue: 0.6111 time to fit residues: 216.3798 Evaluate side-chains 315 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 0.1980 chunk 134 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN G 81 GLN C 18 HIS E 60 ASN I 81 GLN D 18 HIS F 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114431 restraints weight = 31030.993| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.80 r_work: 0.3453 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17952 Z= 0.132 Angle : 0.621 10.249 24414 Z= 0.306 Chirality : 0.047 0.381 2772 Planarity : 0.004 0.049 3069 Dihedral : 6.376 55.788 3510 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.51 % Allowed : 27.24 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.18), residues: 2124 helix: 1.15 (0.26), residues: 372 sheet: -0.63 (0.22), residues: 507 loop : -0.75 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 76 TYR 0.014 0.001 TYR I 79 PHE 0.041 0.002 PHE A 147 TRP 0.007 0.001 TRP J 35 HIS 0.004 0.001 HIS F 64 Details of bonding type rmsd covalent geometry : bond 0.00296 (17871) covalent geometry : angle 0.60126 (24195) SS BOND : bond 0.00319 ( 24) SS BOND : angle 1.63749 ( 48) hydrogen bonds : bond 0.04116 ( 614) hydrogen bonds : angle 5.58080 ( 1734) link_BETA1-4 : bond 0.00534 ( 21) link_BETA1-4 : angle 1.97872 ( 63) link_BETA1-6 : bond 0.00158 ( 3) link_BETA1-6 : angle 1.34960 ( 9) link_NAG-ASN : bond 0.00302 ( 33) link_NAG-ASN : angle 1.67048 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8181 (p) REVERT: H 64 LYS cc_start: 0.8710 (tttm) cc_final: 0.8478 (ttpp) REVERT: H 68 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7602 (m) REVERT: H 81 GLN cc_start: 0.6707 (tp-100) cc_final: 0.6457 (tp40) REVERT: H 105 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7096 (pp30) REVERT: L 31 HIS cc_start: 0.7540 (p-80) cc_final: 0.7079 (p-80) REVERT: A 33 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7748 (ttm110) REVERT: A 62 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: A 70 LEU cc_start: 0.7939 (tp) cc_final: 0.7706 (tp) REVERT: A 77 ASP cc_start: 0.7538 (m-30) cc_final: 0.7007 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: G 1 GLN cc_start: 0.7354 (mt0) cc_final: 0.6786 (mt0) REVERT: G 64 LYS cc_start: 0.8721 (tttm) cc_final: 0.8510 (ttpp) REVERT: G 68 THR cc_start: 0.7792 (t) cc_final: 0.7573 (m) REVERT: G 82 MET cc_start: 0.8272 (mtm) cc_final: 0.8045 (mtt) REVERT: G 105 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7114 (pp30) REVERT: J 31 HIS cc_start: 0.7803 (p-80) cc_final: 0.7266 (p-80) REVERT: J 47 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7666 (mmm) REVERT: C 70 LEU cc_start: 0.7980 (tp) cc_final: 0.7684 (tp) REVERT: C 77 ASP cc_start: 0.7512 (m-30) cc_final: 0.7084 (OUTLIER) REVERT: C 201 ARG cc_start: 0.6986 (mtm180) cc_final: 0.6711 (mtm-85) REVERT: C 220 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8238 (mtt90) REVERT: C 246 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (t0) REVERT: E 143 LYS cc_start: 0.6369 (mttt) cc_final: 0.6093 (mttp) REVERT: I 1 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6788 (mt0) REVERT: I 64 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8104 (tttt) REVERT: I 105 GLN cc_start: 0.7219 (pp30) cc_final: 0.7012 (pp30) REVERT: K 31 HIS cc_start: 0.7892 (p-80) cc_final: 0.7348 (p-80) REVERT: D 33 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7688 (ttm110) REVERT: D 62 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: D 70 LEU cc_start: 0.8039 (tp) cc_final: 0.7740 (tp) REVERT: D 77 ASP cc_start: 0.7563 (m-30) cc_final: 0.7222 (OUTLIER) REVERT: D 83 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8565 (mtmm) outliers start: 64 outliers final: 41 residues processed: 304 average time/residue: 0.5682 time to fit residues: 194.6158 Evaluate side-chains 288 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 18 HIS C 210 GLN E 60 ASN D 18 HIS F 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113062 restraints weight = 31140.015| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.81 r_work: 0.3429 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17952 Z= 0.177 Angle : 0.648 10.575 24414 Z= 0.322 Chirality : 0.047 0.339 2772 Planarity : 0.004 0.049 3069 Dihedral : 6.269 56.004 3507 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.84 % Allowed : 26.96 % Favored : 69.19 % 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: -0.66 (0.17), residues: 2124 helix: 1.17 (0.26), residues: 372 sheet: -0.57 (0.24), residues: 465 loop : -0.87 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 76 TYR 0.014 0.001 TYR I 79 PHE 0.046 0.002 PHE A 147 TRP 0.006 0.001 TRP C 234 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00402 (17871) covalent geometry : angle 0.62852 (24195) SS BOND : bond 0.00476 ( 24) SS BOND : angle 1.79895 ( 48) hydrogen bonds : bond 0.04275 ( 614) hydrogen bonds : angle 5.63293 ( 1734) link_BETA1-4 : bond 0.00525 ( 21) link_BETA1-4 : angle 1.94462 ( 63) link_BETA1-6 : bond 0.00154 ( 3) link_BETA1-6 : angle 1.27972 ( 9) link_NAG-ASN : bond 0.00319 ( 33) link_NAG-ASN : angle 1.73357 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7526 (mt0) cc_final: 0.7061 (mt0) REVERT: H 64 LYS cc_start: 0.8705 (tttm) cc_final: 0.8476 (ttpp) REVERT: H 68 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7652 (m) REVERT: H 105 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7064 (pp30) REVERT: L 31 HIS cc_start: 0.7579 (p-80) cc_final: 0.7224 (p-80) REVERT: A 62 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: A 70 LEU cc_start: 0.7929 (tp) cc_final: 0.7724 (tp) REVERT: A 77 ASP cc_start: 0.7547 (m-30) cc_final: 0.7048 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: B 133 MET cc_start: 0.7736 (mtp) cc_final: 0.7418 (mtm) REVERT: G 1 GLN cc_start: 0.7295 (mt0) cc_final: 0.6717 (mt0) REVERT: G 68 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7625 (m) REVERT: G 82 MET cc_start: 0.8267 (mtm) cc_final: 0.8039 (mtt) REVERT: G 105 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7084 (pp30) REVERT: J 31 HIS cc_start: 0.7830 (p-80) cc_final: 0.7287 (p-80) REVERT: J 47 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7658 (mmm) REVERT: C 70 LEU cc_start: 0.8023 (tp) cc_final: 0.7752 (tp) REVERT: C 77 ASP cc_start: 0.7531 (m-30) cc_final: 0.7129 (OUTLIER) REVERT: C 201 ARG cc_start: 0.7035 (mtm180) cc_final: 0.6777 (mtm-85) REVERT: C 220 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8229 (mtt90) REVERT: C 246 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8720 (t0) REVERT: E 143 LYS cc_start: 0.6461 (mttt) cc_final: 0.6184 (mttp) REVERT: I 1 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6765 (mt0) REVERT: I 64 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8088 (tttt) REVERT: K 31 HIS cc_start: 0.7900 (p-80) cc_final: 0.7531 (p-80) REVERT: D 33 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7627 (ttm110) REVERT: D 62 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: D 70 LEU cc_start: 0.8080 (tp) cc_final: 0.7778 (tp) REVERT: D 77 ASP cc_start: 0.7574 (m-30) cc_final: 0.7215 (OUTLIER) REVERT: D 201 ARG cc_start: 0.6953 (mtm180) cc_final: 0.6609 (mtm-85) REVERT: D 244 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8492 (tt) outliers start: 70 outliers final: 50 residues processed: 281 average time/residue: 0.5815 time to fit residues: 184.0695 Evaluate side-chains 295 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 140 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN A 18 HIS B 60 ASN G 81 GLN C 18 HIS E 60 ASN D 18 HIS F 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113231 restraints weight = 30845.121| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.77 r_work: 0.3443 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17952 Z= 0.163 Angle : 0.645 11.887 24414 Z= 0.319 Chirality : 0.047 0.329 2772 Planarity : 0.004 0.049 3069 Dihedral : 6.203 55.958 3507 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.84 % Allowed : 27.02 % Favored : 69.14 % 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: -0.63 (0.17), residues: 2124 helix: 1.14 (0.26), residues: 372 sheet: -0.37 (0.24), residues: 444 loop : -0.91 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 76 TYR 0.014 0.001 TYR I 79 PHE 0.047 0.002 PHE A 147 TRP 0.006 0.001 TRP J 35 HIS 0.004 0.001 HIS F 64 Details of bonding type rmsd covalent geometry : bond 0.00371 (17871) covalent geometry : angle 0.62576 (24195) SS BOND : bond 0.00369 ( 24) SS BOND : angle 1.86831 ( 48) hydrogen bonds : bond 0.04218 ( 614) hydrogen bonds : angle 5.62877 ( 1734) link_BETA1-4 : bond 0.00529 ( 21) link_BETA1-4 : angle 1.83824 ( 63) link_BETA1-6 : bond 0.00144 ( 3) link_BETA1-6 : angle 1.29522 ( 9) link_NAG-ASN : bond 0.00316 ( 33) link_NAG-ASN : angle 1.69829 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7584 (mt0) cc_final: 0.7090 (mt0) REVERT: H 12 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8146 (p) REVERT: H 64 LYS cc_start: 0.8706 (tttm) cc_final: 0.8462 (ttpp) REVERT: H 68 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7676 (m) REVERT: L 31 HIS cc_start: 0.7772 (p-80) cc_final: 0.7412 (p-80) REVERT: A 62 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: A 77 ASP cc_start: 0.7689 (m-30) cc_final: 0.7101 (OUTLIER) REVERT: A 197 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: B 133 MET cc_start: 0.7728 (mtp) cc_final: 0.7409 (mtm) REVERT: G 1 GLN cc_start: 0.7383 (mt0) cc_final: 0.6799 (mt0) REVERT: G 68 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7607 (m) REVERT: G 105 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7099 (pp30) REVERT: J 31 HIS cc_start: 0.8036 (p-80) cc_final: 0.7491 (p-80) REVERT: J 47 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7826 (mmm) REVERT: C 70 LEU cc_start: 0.8097 (tp) cc_final: 0.7844 (tp) REVERT: C 201 ARG cc_start: 0.7258 (mtm180) cc_final: 0.7003 (mtm-85) REVERT: C 220 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8231 (mtt90) REVERT: C 246 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8753 (t0) REVERT: E 143 LYS cc_start: 0.6531 (mttt) cc_final: 0.6196 (mttp) REVERT: I 1 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6814 (mt0) REVERT: I 64 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8105 (tttt) REVERT: I 105 GLN cc_start: 0.7131 (pp30) cc_final: 0.6886 (pp30) REVERT: K 31 HIS cc_start: 0.8078 (p-80) cc_final: 0.7721 (p-80) REVERT: D 33 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7679 (ttm110) REVERT: D 62 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: D 70 LEU cc_start: 0.8148 (tp) cc_final: 0.7844 (tp) REVERT: D 201 ARG cc_start: 0.7150 (mtm180) cc_final: 0.6804 (mtm-85) REVERT: D 244 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8571 (tt) REVERT: D 295 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7442 (pt0) outliers start: 70 outliers final: 48 residues processed: 280 average time/residue: 0.6012 time to fit residues: 189.1564 Evaluate side-chains 296 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 139 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 203 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 60 ASN C 18 HIS ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN D 18 HIS F 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114896 restraints weight = 30671.662| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.72 r_work: 0.3479 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17952 Z= 0.152 Angle : 0.636 10.447 24414 Z= 0.315 Chirality : 0.047 0.326 2772 Planarity : 0.004 0.049 3069 Dihedral : 6.128 55.926 3507 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.79 % Allowed : 27.40 % Favored : 68.81 % 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: -0.60 (0.18), residues: 2124 helix: 1.13 (0.26), residues: 372 sheet: -0.31 (0.24), residues: 444 loop : -0.89 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 76 TYR 0.013 0.001 TYR I 79 PHE 0.046 0.002 PHE A 147 TRP 0.006 0.001 TRP J 35 HIS 0.004 0.001 HIS F 64 Details of bonding type rmsd covalent geometry : bond 0.00347 (17871) covalent geometry : angle 0.61832 (24195) SS BOND : bond 0.00363 ( 24) SS BOND : angle 1.79026 ( 48) hydrogen bonds : bond 0.04158 ( 614) hydrogen bonds : angle 5.59871 ( 1734) link_BETA1-4 : bond 0.00531 ( 21) link_BETA1-4 : angle 1.71952 ( 63) link_BETA1-6 : bond 0.00160 ( 3) link_BETA1-6 : angle 1.30700 ( 9) link_NAG-ASN : bond 0.00325 ( 33) link_NAG-ASN : angle 1.67069 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6553.95 seconds wall clock time: 112 minutes 49.47 seconds (6769.47 seconds total)