Starting phenix.real_space_refine on Wed Mar 4 21:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y1z_10673/03_2026/6y1z_10673.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y1z_10673/03_2026/6y1z_10673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y1z_10673/03_2026/6y1z_10673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y1z_10673/03_2026/6y1z_10673.map" model { file = "/net/cci-nas-00/data/ceres_data/6y1z_10673/03_2026/6y1z_10673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y1z_10673/03_2026/6y1z_10673.cif" } resolution = 2.82 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= 0.012 sd= 0.113 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 45 5.16 5 C 10935 2.51 5 N 2670 2.21 5 O 2960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s 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: 16610 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "D" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "B" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "C" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "E" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="O7B C 501 " pdbres="TRP C 502 " Chain: "C" 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: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="O7B E 501 " pdbres="TRP E 502 " 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 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ATYR A 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 67 " occ=0.50 residue: pdb=" N ATRP A 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 168 " occ=0.50 residue: pdb=" N ATYR D 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 67 " occ=0.50 residue: pdb=" N ATRP D 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP D 168 " occ=0.50 residue: pdb=" N ATYR B 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 67 " occ=0.50 residue: pdb=" N ATRP B 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 168 " occ=0.50 residue: pdb=" N ATYR C 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 67 " occ=0.50 residue: pdb=" N ATRP C 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP C 168 " occ=0.50 residue: pdb=" N ATYR E 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 67 " occ=0.50 residue: pdb=" N ATRP E 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP E 168 " occ=0.50 Time building chain proxies: 7.24, per 1000 atoms: 0.44 Number of scatterers: 16610 At special positions: 0 Unit cell: (101.365, 103.499, 168.586, 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 45 16.00 O 2960 8.00 N 2670 7.00 C 10935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 503 " - " ASN A 82 " " NAG B 503 " - " ASN B 82 " " NAG C 504 " - " ASN C 82 " " NAG D 503 " - " ASN D 82 " " NAG E 504 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN D 164 " " NAG I 1 " - " ASN D 148 " " NAG J 1 " - " ASN B 164 " " NAG K 1 " - " ASN B 148 " " NAG L 1 " - " ASN C 164 " " NAG M 1 " - " ASN C 148 " " NAG N 1 " - " ASN E 164 " " NAG O 1 " - " ASN E 148 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 44.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.544A pdb=" N ALA A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 242 removed outlier: 4.471A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 243 through 244 No H-bonds generated for 'chain 'A' and resid 243 through 244' Processing helix chain 'A' and resid 245 through 249 removed outlier: 4.370A pdb=" N GLY A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.891A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 398 through 458 Processing helix chain 'D' and resid 12 through 21 removed outlier: 3.545A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 223 through 242 removed outlier: 4.472A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 243 through 244 No H-bonds generated for 'chain 'D' and resid 243 through 244' Processing helix chain 'D' and resid 245 through 249 removed outlier: 4.370A pdb=" N GLY D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 282 through 309 removed outlier: 3.890A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 398 through 458 Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.544A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 223 through 242 removed outlier: 4.471A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 243 through 244 No H-bonds generated for 'chain 'B' and resid 243 through 244' Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.369A pdb=" N GLY B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.891A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 398 through 458 Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.544A pdb=" N ALA C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 223 through 242 removed outlier: 4.472A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 243 through 244 No H-bonds generated for 'chain 'C' and resid 243 through 244' Processing helix chain 'C' and resid 245 through 249 removed outlier: 4.371A pdb=" N GLY C 249 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 Processing helix chain 'C' and resid 282 through 309 removed outlier: 3.891A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 398 through 458 Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.544A pdb=" N ALA E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 223 through 242 removed outlier: 4.472A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 243 through 244 No H-bonds generated for 'chain 'E' and resid 243 through 244' Processing helix chain 'E' and resid 245 through 249 removed outlier: 4.371A pdb=" N GLY E 249 " --> pdb=" O PRO E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 270 Processing helix chain 'E' and resid 282 through 309 removed outlier: 3.892A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 329 Processing helix chain 'E' and resid 398 through 458 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.953A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ATYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP A 42 " --> pdb=" O ATYR A 67 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 164 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.109A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.955A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ATYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP D 42 " --> pdb=" O ATYR D 67 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN D 164 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.108A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.954A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ATYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASP B 42 " --> pdb=" O ATYR B 67 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 164 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.109A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.954A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ATYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASP C 42 " --> pdb=" O ATYR C 67 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 164 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.109A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.954A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ATYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASP E 42 " --> pdb=" O ATYR E 67 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN E 164 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.108A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2555 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: 1.88 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4239 1.33 - 1.45: 3326 1.45 - 1.57: 9450 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17085 Sorted by residual: bond pdb=" C21 O7B A 504 " pdb=" C22 O7B A 504 " ideal model delta sigma weight residual 1.554 1.521 0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" C21 O7B D 504 " pdb=" C22 O7B D 504 " ideal model delta sigma weight residual 1.554 1.521 0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C21 O7B E 501 " pdb=" C22 O7B E 501 " ideal model delta sigma weight residual 1.554 1.522 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C21 O7B C 501 " pdb=" C22 O7B C 501 " ideal model delta sigma weight residual 1.554 1.522 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C21 O7B B 504 " pdb=" C22 O7B B 504 " ideal model delta sigma weight residual 1.554 1.522 0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 17080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 22917 1.62 - 3.25: 365 3.25 - 4.87: 43 4.87 - 6.50: 25 6.50 - 8.12: 15 Bond angle restraints: 23365 Sorted by residual: angle pdb=" C06 O7B B 504 " pdb=" N05 O7B B 504 " pdb=" C15 O7B B 504 " ideal model delta sigma weight residual 116.43 124.55 -8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" C06 O7B E 501 " pdb=" N05 O7B E 501 " pdb=" C15 O7B E 501 " ideal model delta sigma weight residual 116.43 124.52 -8.09 3.00e+00 1.11e-01 7.28e+00 angle pdb=" C06 O7B C 501 " pdb=" N05 O7B C 501 " pdb=" C15 O7B C 501 " ideal model delta sigma weight residual 116.43 124.51 -8.08 3.00e+00 1.11e-01 7.26e+00 angle pdb=" C06 O7B D 504 " pdb=" N05 O7B D 504 " pdb=" C15 O7B D 504 " ideal model delta sigma weight residual 116.43 124.50 -8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" C06 O7B A 504 " pdb=" N05 O7B A 504 " pdb=" C15 O7B A 504 " ideal model delta sigma weight residual 116.43 124.48 -8.05 3.00e+00 1.11e-01 7.21e+00 ... (remaining 23360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 9997 21.52 - 43.04: 393 43.04 - 64.56: 90 64.56 - 86.09: 69 86.09 - 107.61: 26 Dihedral angle restraints: 10575 sinusoidal: 4780 harmonic: 5795 Sorted by residual: dihedral pdb=" C2 NAG M 2 " pdb=" C3 NAG M 2 " pdb=" C4 NAG M 2 " pdb=" C5 NAG M 2 " ideal model delta sinusoidal sigma weight residual 53.78 -53.83 107.61 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG K 2 " pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" C5 NAG K 2 " ideal model delta sinusoidal sigma weight residual 53.78 -53.80 107.58 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG G 2 " pdb=" C3 NAG G 2 " pdb=" C4 NAG G 2 " pdb=" C5 NAG G 2 " ideal model delta sinusoidal sigma weight residual 53.78 -53.79 107.57 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 10572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2579 0.094 - 0.187: 181 0.187 - 0.281: 10 0.281 - 0.374: 0 0.374 - 0.468: 5 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C15 O7B E 501 " pdb=" C16 O7B E 501 " pdb=" C20 O7B E 501 " pdb=" N05 O7B E 501 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C15 O7B B 504 " pdb=" C16 O7B B 504 " pdb=" C20 O7B B 504 " pdb=" N05 O7B B 504 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C15 O7B D 504 " pdb=" C16 O7B D 504 " pdb=" C20 O7B D 504 " pdb=" N05 O7B D 504 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2772 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 O7B E 501 " -0.020 2.00e-02 2.50e+03 1.51e-02 3.42e+00 pdb=" C06 O7B E 501 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B E 501 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B E 501 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B E 501 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B E 501 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 O7B D 504 " -0.020 2.00e-02 2.50e+03 1.50e-02 3.37e+00 pdb=" C06 O7B D 504 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B D 504 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B D 504 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B D 504 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B D 504 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 O7B C 501 " -0.020 2.00e-02 2.50e+03 1.48e-02 3.30e+00 pdb=" C06 O7B C 501 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B C 501 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B C 501 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B C 501 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B C 501 " -0.022 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5143 2.84 - 3.36: 14866 3.36 - 3.87: 27276 3.87 - 4.39: 30178 4.39 - 4.90: 54112 Nonbonded interactions: 131575 Sorted by model distance: nonbonded pdb=" OD1 ASP D 105 " pdb=" N VAL D 106 " model vdw 2.325 3.120 nonbonded pdb=" OD1 ASP B 105 " pdb=" N VAL B 106 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP E 105 " pdb=" N VAL E 106 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP A 105 " pdb=" N VAL A 106 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP C 105 " pdb=" N VAL C 106 " model vdw 2.326 3.120 ... (remaining 131570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'B' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'C' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'D' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'E' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.320 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.003 0.033 17120 Z= 0.167 Angle : 0.580 8.122 23465 Z= 0.293 Chirality : 0.049 0.468 2775 Planarity : 0.003 0.034 2820 Dihedral : 15.307 107.607 6790 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.49 % Allowed : 4.70 % Favored : 92.82 % 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: -1.37 (0.18), residues: 1930 helix: 1.38 (0.18), residues: 745 sheet: -2.65 (0.18), residues: 470 loop : -2.08 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.007 0.001 TYR B 64 PHE 0.006 0.001 PHE C 222 TRP 0.005 0.001 TRP E 426 HIS 0.001 0.000 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00320 (17085) covalent geometry : angle 0.57667 (23365) SS BOND : bond 0.00083 ( 5) SS BOND : angle 0.32277 ( 10) hydrogen bonds : bond 0.13942 ( 860) hydrogen bonds : angle 5.68966 ( 2555) link_BETA1-4 : bond 0.00481 ( 15) link_BETA1-4 : angle 1.22262 ( 45) link_NAG-ASN : bond 0.00067 ( 15) link_NAG-ASN : angle 1.16985 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7915 (t0) cc_final: 0.7303 (t0) REVERT: A 54 LYS cc_start: 0.8481 (tttm) cc_final: 0.8253 (tttm) REVERT: A 105 ASP cc_start: 0.8445 (t0) cc_final: 0.8000 (t0) REVERT: A 108 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7813 (mtpp) REVERT: A 144 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: A 416 ARG cc_start: 0.6545 (mtp180) cc_final: 0.6022 (mmp-170) REVERT: A 421 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6522 (tt0) REVERT: A 456 TRP cc_start: 0.6847 (t60) cc_final: 0.5458 (t-100) REVERT: D 52 ASP cc_start: 0.7955 (t0) cc_final: 0.7293 (t0) REVERT: D 54 LYS cc_start: 0.8474 (tttm) cc_final: 0.8185 (tptm) REVERT: D 122 GLU cc_start: 0.7804 (mp0) cc_final: 0.7470 (mp0) REVERT: D 144 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: D 416 ARG cc_start: 0.6482 (mtp180) cc_final: 0.6074 (mmp-170) REVERT: D 421 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: D 456 TRP cc_start: 0.6716 (t60) cc_final: 0.5494 (t-100) REVERT: B 52 ASP cc_start: 0.7835 (t0) cc_final: 0.6695 (t0) REVERT: B 54 LYS cc_start: 0.8593 (tttm) cc_final: 0.8358 (tttm) REVERT: B 55 ASN cc_start: 0.8670 (m110) cc_final: 0.7821 (m110) REVERT: B 105 ASP cc_start: 0.8469 (t0) cc_final: 0.8147 (t0) REVERT: B 416 ARG cc_start: 0.6476 (mtp180) cc_final: 0.6147 (mmp-170) REVERT: B 421 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: B 456 TRP cc_start: 0.6583 (t60) cc_final: 0.5383 (t-100) REVERT: C 52 ASP cc_start: 0.7866 (t0) cc_final: 0.6889 (t0) REVERT: C 54 LYS cc_start: 0.8441 (tttm) cc_final: 0.8124 (tptm) REVERT: C 55 ASN cc_start: 0.8545 (m110) cc_final: 0.8040 (m110) REVERT: C 108 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7943 (mtpp) REVERT: C 456 TRP cc_start: 0.6784 (t60) cc_final: 0.5668 (t-100) REVERT: E 54 LYS cc_start: 0.8465 (tttm) cc_final: 0.8200 (tptm) REVERT: E 55 ASN cc_start: 0.8683 (m110) cc_final: 0.8419 (m110) REVERT: E 416 ARG cc_start: 0.6314 (mtp180) cc_final: 0.5862 (mmp-170) REVERT: E 421 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6421 (tt0) REVERT: E 456 TRP cc_start: 0.6600 (t60) cc_final: 0.5339 (t-100) outliers start: 40 outliers final: 12 residues processed: 237 average time/residue: 0.5402 time to fit residues: 143.2227 Evaluate side-chains 140 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 125 ASN D 22 ASN B 101 ASN B 125 ASN C 22 ASN C 111 ASN C 125 ASN E 22 ASN E 66 GLN E 125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085503 restraints weight = 66190.566| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.77 r_work: 0.2801 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17120 Z= 0.107 Angle : 0.566 8.293 23465 Z= 0.273 Chirality : 0.045 0.191 2775 Planarity : 0.004 0.036 2820 Dihedral : 11.934 71.112 3004 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.60 % Allowed : 10.33 % Favored : 87.07 % 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: -0.26 (0.19), residues: 1930 helix: 2.44 (0.18), residues: 745 sheet: -2.36 (0.20), residues: 485 loop : -1.37 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 328 TYR 0.013 0.001 TYR D 64 PHE 0.008 0.001 PHE E 233 TRP 0.010 0.001 TRP E 68 HIS 0.001 0.000 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00217 (17085) covalent geometry : angle 0.56021 (23365) SS BOND : bond 0.00351 ( 5) SS BOND : angle 1.18028 ( 10) hydrogen bonds : bond 0.04837 ( 860) hydrogen bonds : angle 4.47462 ( 2555) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 1.73071 ( 45) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.03151 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8509 (mt) cc_final: 0.8283 (mp) REVERT: A 52 ASP cc_start: 0.6857 (t0) cc_final: 0.6306 (t0) REVERT: A 54 LYS cc_start: 0.8204 (tttm) cc_final: 0.7997 (tttm) REVERT: A 105 ASP cc_start: 0.8662 (t0) cc_final: 0.8106 (t0) REVERT: A 108 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7207 (mtpp) REVERT: A 144 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: A 210 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8443 (tpp) REVERT: A 223 TYR cc_start: 0.7327 (m-80) cc_final: 0.7030 (m-80) REVERT: A 291 MET cc_start: 0.5981 (tmm) cc_final: 0.5686 (tpp) REVERT: A 421 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: A 456 TRP cc_start: 0.5876 (t60) cc_final: 0.4731 (t-100) REVERT: D 52 ASP cc_start: 0.7030 (t0) cc_final: 0.6488 (t0) REVERT: D 54 LYS cc_start: 0.8398 (tttm) cc_final: 0.8157 (tptm) REVERT: D 144 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: D 223 TYR cc_start: 0.6848 (m-80) cc_final: 0.6589 (m-80) REVERT: D 416 ARG cc_start: 0.6136 (mtp180) cc_final: 0.5665 (mmp-170) REVERT: D 421 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6101 (tt0) REVERT: D 456 TRP cc_start: 0.5841 (t60) cc_final: 0.4762 (t-100) REVERT: B 52 ASP cc_start: 0.7154 (t0) cc_final: 0.6897 (t70) REVERT: B 105 ASP cc_start: 0.8834 (t0) cc_final: 0.8471 (t0) REVERT: B 199 PHE cc_start: 0.6679 (t80) cc_final: 0.6342 (t80) REVERT: B 291 MET cc_start: 0.7187 (ttp) cc_final: 0.6365 (ttp) REVERT: B 416 ARG cc_start: 0.6236 (mtp180) cc_final: 0.5731 (mmp-170) REVERT: B 421 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6005 (tt0) REVERT: B 456 TRP cc_start: 0.5797 (t60) cc_final: 0.4769 (t-100) REVERT: C 210 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8413 (tpp) REVERT: C 421 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5782 (tp30) REVERT: C 456 TRP cc_start: 0.5985 (t60) cc_final: 0.5009 (t-100) REVERT: E 35 LYS cc_start: 0.7593 (mmtt) cc_final: 0.6819 (tttp) REVERT: E 199 PHE cc_start: 0.6889 (t80) cc_final: 0.6551 (t80) REVERT: E 223 TYR cc_start: 0.7184 (m-80) cc_final: 0.6809 (m-80) REVERT: E 416 ARG cc_start: 0.5967 (mtp180) cc_final: 0.5450 (mmp-170) REVERT: E 421 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: E 456 TRP cc_start: 0.5748 (t60) cc_final: 0.4638 (t-100) outliers start: 42 outliers final: 19 residues processed: 164 average time/residue: 0.5208 time to fit residues: 96.7148 Evaluate side-chains 135 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 174 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 22 ASN D 55 ASN B 55 ASN C 22 ASN C 55 ASN C 111 ASN E 22 ASN E 50 ASN E 55 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085627 restraints weight = 61374.093| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.67 r_work: 0.2813 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17120 Z= 0.108 Angle : 0.526 7.604 23465 Z= 0.254 Chirality : 0.043 0.134 2775 Planarity : 0.004 0.037 2820 Dihedral : 7.298 64.520 3001 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.04 % Allowed : 10.11 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1930 helix: 2.89 (0.18), residues: 745 sheet: -2.00 (0.21), residues: 485 loop : -0.86 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.012 0.001 TYR E 64 PHE 0.007 0.001 PHE A 254 TRP 0.013 0.001 TRP B 320 HIS 0.001 0.000 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00230 (17085) covalent geometry : angle 0.51946 (23365) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.11575 ( 10) hydrogen bonds : bond 0.04491 ( 860) hydrogen bonds : angle 4.12840 ( 2555) link_BETA1-4 : bond 0.00473 ( 15) link_BETA1-4 : angle 1.52018 ( 45) link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 1.22552 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8525 (mt) cc_final: 0.8310 (mp) REVERT: A 52 ASP cc_start: 0.6929 (t0) cc_final: 0.6069 (t0) REVERT: A 54 LYS cc_start: 0.8240 (tttm) cc_final: 0.7940 (tttm) REVERT: A 105 ASP cc_start: 0.8725 (t0) cc_final: 0.8135 (t0) REVERT: A 144 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: A 223 TYR cc_start: 0.7410 (m-80) cc_final: 0.7126 (m-80) REVERT: A 291 MET cc_start: 0.6010 (tmm) cc_final: 0.5646 (tpp) REVERT: A 421 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6107 (tt0) REVERT: A 456 TRP cc_start: 0.5890 (t60) cc_final: 0.4719 (t-100) REVERT: D 52 ASP cc_start: 0.7077 (t0) cc_final: 0.6437 (t0) REVERT: D 54 LYS cc_start: 0.8375 (tttm) cc_final: 0.8112 (tptm) REVERT: D 108 LYS cc_start: 0.7686 (mtmp) cc_final: 0.7325 (mtpp) REVERT: D 223 TYR cc_start: 0.6905 (m-80) cc_final: 0.6628 (m-80) REVERT: D 416 ARG cc_start: 0.6172 (mtp180) cc_final: 0.5682 (mmp-170) REVERT: D 421 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6111 (tt0) REVERT: D 456 TRP cc_start: 0.5834 (t60) cc_final: 0.4759 (t-100) REVERT: B 41 ILE cc_start: 0.8625 (mt) cc_final: 0.8390 (mp) REVERT: B 52 ASP cc_start: 0.7205 (t0) cc_final: 0.6920 (t70) REVERT: B 60 THR cc_start: 0.8383 (p) cc_final: 0.8017 (t) REVERT: B 105 ASP cc_start: 0.8817 (t0) cc_final: 0.8339 (t0) REVERT: B 199 PHE cc_start: 0.6699 (t80) cc_final: 0.6268 (t80) REVERT: B 291 MET cc_start: 0.7100 (ttp) cc_final: 0.6298 (ttp) REVERT: B 416 ARG cc_start: 0.6306 (mtp180) cc_final: 0.5746 (mmp-170) REVERT: B 421 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: B 456 TRP cc_start: 0.5805 (t60) cc_final: 0.4793 (t-100) REVERT: C 41 ILE cc_start: 0.8485 (mt) cc_final: 0.8014 (pt) REVERT: C 421 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5630 (tt0) REVERT: C 456 TRP cc_start: 0.5974 (t60) cc_final: 0.4989 (t-100) REVERT: E 199 PHE cc_start: 0.6918 (t80) cc_final: 0.6600 (t80) REVERT: E 223 TYR cc_start: 0.7185 (m-80) cc_final: 0.6825 (m-80) REVERT: E 291 MET cc_start: 0.7131 (tpp) cc_final: 0.6501 (ttp) REVERT: E 416 ARG cc_start: 0.5940 (mtp180) cc_final: 0.5410 (mmp-170) REVERT: E 421 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6103 (tt0) REVERT: E 456 TRP cc_start: 0.5744 (t60) cc_final: 0.4619 (t-100) outliers start: 50 outliers final: 22 residues processed: 165 average time/residue: 0.5265 time to fit residues: 98.3197 Evaluate side-chains 141 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 154 optimal weight: 0.0570 chunk 125 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 50 ASN C 22 ASN E 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.083350 restraints weight = 76667.397| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 5.07 r_work: 0.2761 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17120 Z= 0.141 Angle : 0.542 8.962 23465 Z= 0.263 Chirality : 0.044 0.136 2775 Planarity : 0.004 0.038 2820 Dihedral : 6.472 62.869 2999 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.82 % Allowed : 11.33 % Favored : 85.86 % 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: 0.68 (0.20), residues: 1930 helix: 3.02 (0.18), residues: 745 sheet: -1.84 (0.21), residues: 490 loop : -0.60 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 328 TYR 0.016 0.001 TYR C 64 PHE 0.009 0.001 PHE D 222 TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00331 (17085) covalent geometry : angle 0.53476 (23365) SS BOND : bond 0.00262 ( 5) SS BOND : angle 0.99809 ( 10) hydrogen bonds : bond 0.04624 ( 860) hydrogen bonds : angle 4.08453 ( 2555) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.55432 ( 45) link_NAG-ASN : bond 0.00191 ( 15) link_NAG-ASN : angle 1.36042 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8513 (mt) cc_final: 0.8293 (mp) REVERT: A 105 ASP cc_start: 0.8742 (t0) cc_final: 0.8221 (t0) REVERT: A 144 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: A 223 TYR cc_start: 0.7315 (m-80) cc_final: 0.7013 (m-80) REVERT: A 416 ARG cc_start: 0.6287 (mtp180) cc_final: 0.5715 (mmp-170) REVERT: A 421 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6116 (tt0) REVERT: A 456 TRP cc_start: 0.5787 (t60) cc_final: 0.4595 (t-100) REVERT: D 52 ASP cc_start: 0.7064 (t0) cc_final: 0.6469 (t0) REVERT: D 54 LYS cc_start: 0.8318 (tttm) cc_final: 0.8066 (tptm) REVERT: D 108 LYS cc_start: 0.7608 (mtmp) cc_final: 0.7167 (mtpp) REVERT: D 144 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: D 223 TYR cc_start: 0.6828 (m-80) cc_final: 0.6564 (m-80) REVERT: D 311 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7095 (pm20) REVERT: D 416 ARG cc_start: 0.6181 (mtp180) cc_final: 0.5770 (mmp-170) REVERT: D 421 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6132 (tt0) REVERT: D 456 TRP cc_start: 0.5736 (t60) cc_final: 0.4584 (t-100) REVERT: B 41 ILE cc_start: 0.8623 (mt) cc_final: 0.8386 (mp) REVERT: B 52 ASP cc_start: 0.7146 (t0) cc_final: 0.6805 (t70) REVERT: B 60 THR cc_start: 0.8387 (p) cc_final: 0.8037 (t) REVERT: B 105 ASP cc_start: 0.8858 (t0) cc_final: 0.8357 (t0) REVERT: B 199 PHE cc_start: 0.6778 (t80) cc_final: 0.6393 (t80) REVERT: B 223 TYR cc_start: 0.7249 (m-80) cc_final: 0.6940 (m-80) REVERT: B 291 MET cc_start: 0.7060 (ttp) cc_final: 0.6186 (ttp) REVERT: B 416 ARG cc_start: 0.6104 (mtp180) cc_final: 0.5521 (mmp-170) REVERT: B 421 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6007 (tt0) REVERT: B 456 TRP cc_start: 0.5835 (t60) cc_final: 0.4797 (t-100) REVERT: C 291 MET cc_start: 0.6324 (tmm) cc_final: 0.6061 (tpt) REVERT: C 421 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5719 (tp30) REVERT: C 456 TRP cc_start: 0.5956 (t60) cc_final: 0.4987 (t-100) REVERT: E 105 ASP cc_start: 0.8773 (t0) cc_final: 0.8474 (t0) REVERT: E 199 PHE cc_start: 0.6899 (t80) cc_final: 0.6541 (t80) REVERT: E 223 TYR cc_start: 0.7246 (m-80) cc_final: 0.6884 (m-80) REVERT: E 311 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: E 416 ARG cc_start: 0.5959 (mtp180) cc_final: 0.5434 (mmp-170) REVERT: E 421 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6111 (tt0) REVERT: E 456 TRP cc_start: 0.5780 (t60) cc_final: 0.4644 (t-100) outliers start: 46 outliers final: 26 residues processed: 155 average time/residue: 0.5423 time to fit residues: 94.4138 Evaluate side-chains 149 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN D 22 ASN D 50 ASN C 22 ASN C 50 ASN E 22 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083728 restraints weight = 74687.025| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 5.04 r_work: 0.2778 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17120 Z= 0.121 Angle : 0.517 8.889 23465 Z= 0.253 Chirality : 0.043 0.132 2775 Planarity : 0.004 0.039 2820 Dihedral : 6.098 60.260 2999 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.87 % Allowed : 11.93 % Favored : 85.19 % 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: 0.93 (0.20), residues: 1930 helix: 3.20 (0.18), residues: 745 sheet: -1.75 (0.21), residues: 490 loop : -0.39 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.014 0.001 TYR D 64 PHE 0.008 0.001 PHE B 233 TRP 0.009 0.001 TRP A 68 HIS 0.001 0.000 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00276 (17085) covalent geometry : angle 0.51055 (23365) SS BOND : bond 0.00234 ( 5) SS BOND : angle 0.91033 ( 10) hydrogen bonds : bond 0.04512 ( 860) hydrogen bonds : angle 4.02356 ( 2555) link_BETA1-4 : bond 0.00419 ( 15) link_BETA1-4 : angle 1.50078 ( 45) link_NAG-ASN : bond 0.00126 ( 15) link_NAG-ASN : angle 1.33124 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8516 (mt) cc_final: 0.8301 (mp) REVERT: A 105 ASP cc_start: 0.8790 (t0) cc_final: 0.8238 (t0) REVERT: A 144 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: A 223 TYR cc_start: 0.7318 (m-80) cc_final: 0.6935 (m-80) REVERT: A 291 MET cc_start: 0.6016 (tmm) cc_final: 0.5810 (tmm) REVERT: A 416 ARG cc_start: 0.6306 (mtp180) cc_final: 0.5736 (mmp-170) REVERT: A 421 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6099 (tt0) REVERT: A 456 TRP cc_start: 0.5732 (t60) cc_final: 0.4546 (t-100) REVERT: D 52 ASP cc_start: 0.7106 (t0) cc_final: 0.6493 (t0) REVERT: D 54 LYS cc_start: 0.8318 (tttm) cc_final: 0.8063 (tptm) REVERT: D 108 LYS cc_start: 0.7572 (mtmp) cc_final: 0.7211 (mtpp) REVERT: D 144 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: D 223 TYR cc_start: 0.6842 (m-80) cc_final: 0.6564 (m-80) REVERT: D 416 ARG cc_start: 0.6125 (mtp180) cc_final: 0.5694 (mmp-170) REVERT: D 421 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6160 (tt0) REVERT: D 456 TRP cc_start: 0.5759 (t60) cc_final: 0.4594 (t-100) REVERT: B 41 ILE cc_start: 0.8635 (mt) cc_final: 0.8404 (mp) REVERT: B 52 ASP cc_start: 0.7135 (t0) cc_final: 0.6810 (t70) REVERT: B 60 THR cc_start: 0.8387 (p) cc_final: 0.8042 (t) REVERT: B 105 ASP cc_start: 0.8865 (t0) cc_final: 0.8332 (t0) REVERT: B 199 PHE cc_start: 0.6887 (t80) cc_final: 0.6493 (t80) REVERT: B 223 TYR cc_start: 0.7224 (m-80) cc_final: 0.6889 (m-80) REVERT: B 416 ARG cc_start: 0.6202 (mtp180) cc_final: 0.5626 (mmp-170) REVERT: B 421 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5986 (tt0) REVERT: B 456 TRP cc_start: 0.5966 (t60) cc_final: 0.4866 (t-100) REVERT: C 45 MET cc_start: 0.9190 (tpt) cc_final: 0.8868 (tpp) REVERT: C 199 PHE cc_start: 0.6887 (t80) cc_final: 0.6604 (t80) REVERT: C 421 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5660 (tt0) REVERT: C 456 TRP cc_start: 0.5961 (t60) cc_final: 0.4979 (t-100) REVERT: E 199 PHE cc_start: 0.6928 (t80) cc_final: 0.6563 (t80) REVERT: E 223 TYR cc_start: 0.7169 (m-80) cc_final: 0.6800 (m-80) REVERT: E 416 ARG cc_start: 0.5989 (mtp180) cc_final: 0.5460 (mmp-170) REVERT: E 421 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6142 (tt0) REVERT: E 456 TRP cc_start: 0.5812 (t60) cc_final: 0.4703 (t-100) outliers start: 47 outliers final: 31 residues processed: 159 average time/residue: 0.5167 time to fit residues: 92.8224 Evaluate side-chains 155 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 311 GLN C 22 ASN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082706 restraints weight = 72750.189| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.97 r_work: 0.2768 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17120 Z= 0.155 Angle : 0.543 9.456 23465 Z= 0.265 Chirality : 0.044 0.136 2775 Planarity : 0.004 0.042 2820 Dihedral : 6.032 58.438 2999 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.09 % Allowed : 12.38 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.98 (0.20), residues: 1930 helix: 3.19 (0.17), residues: 745 sheet: -1.72 (0.22), residues: 490 loop : -0.29 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.016 0.001 TYR C 64 PHE 0.009 0.001 PHE E 222 TRP 0.007 0.001 TRP A 68 HIS 0.002 0.000 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00370 (17085) covalent geometry : angle 0.53582 (23365) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.92127 ( 10) hydrogen bonds : bond 0.04703 ( 860) hydrogen bonds : angle 4.05822 ( 2555) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 1.54371 ( 45) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 1.44951 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8512 (mt) cc_final: 0.8293 (mp) REVERT: A 144 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: A 223 TYR cc_start: 0.7330 (m-80) cc_final: 0.6932 (m-80) REVERT: A 291 MET cc_start: 0.5939 (tmm) cc_final: 0.5543 (tpp) REVERT: A 416 ARG cc_start: 0.6321 (mtp180) cc_final: 0.5740 (mmp-170) REVERT: A 421 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6106 (tt0) REVERT: A 456 TRP cc_start: 0.5796 (t60) cc_final: 0.4561 (t-100) REVERT: D 52 ASP cc_start: 0.7071 (t0) cc_final: 0.6403 (t0) REVERT: D 54 LYS cc_start: 0.8470 (tttm) cc_final: 0.8257 (tptm) REVERT: D 108 LYS cc_start: 0.7568 (mtmp) cc_final: 0.7194 (mtpp) REVERT: D 223 TYR cc_start: 0.6866 (m-80) cc_final: 0.6560 (m-80) REVERT: D 416 ARG cc_start: 0.6137 (mtp180) cc_final: 0.5775 (mmp-170) REVERT: D 421 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6202 (tt0) REVERT: D 456 TRP cc_start: 0.5757 (t60) cc_final: 0.4548 (t-100) REVERT: B 17 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: B 41 ILE cc_start: 0.8622 (mt) cc_final: 0.8382 (mp) REVERT: B 52 ASP cc_start: 0.7148 (t0) cc_final: 0.6841 (t70) REVERT: B 105 ASP cc_start: 0.8849 (t0) cc_final: 0.8310 (t0) REVERT: B 199 PHE cc_start: 0.6890 (t80) cc_final: 0.6514 (t80) REVERT: B 223 TYR cc_start: 0.7196 (m-80) cc_final: 0.6818 (m-80) REVERT: B 250 GLU cc_start: 0.7196 (pt0) cc_final: 0.6990 (pt0) REVERT: B 291 MET cc_start: 0.7003 (tpp) cc_final: 0.5737 (ttt) REVERT: B 311 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: B 416 ARG cc_start: 0.6040 (mtp180) cc_final: 0.5475 (mmp-170) REVERT: B 421 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5982 (tt0) REVERT: B 456 TRP cc_start: 0.6016 (t60) cc_final: 0.4877 (t-100) REVERT: C 45 MET cc_start: 0.9208 (tpt) cc_final: 0.8928 (tpp) REVERT: C 108 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7225 (mtpp) REVERT: C 199 PHE cc_start: 0.6782 (t80) cc_final: 0.6382 (t80) REVERT: C 416 ARG cc_start: 0.6020 (mtp180) cc_final: 0.5585 (mmp-170) REVERT: C 421 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: C 456 TRP cc_start: 0.5876 (t60) cc_final: 0.4840 (t-100) REVERT: E 199 PHE cc_start: 0.6811 (t80) cc_final: 0.6438 (t80) REVERT: E 223 TYR cc_start: 0.7275 (m-80) cc_final: 0.6969 (m-80) REVERT: E 291 MET cc_start: 0.7118 (tpp) cc_final: 0.5867 (ttt) REVERT: E 311 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: E 416 ARG cc_start: 0.6008 (mtp180) cc_final: 0.5471 (mmp-170) REVERT: E 421 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6172 (tt0) REVERT: E 456 TRP cc_start: 0.5786 (t60) cc_final: 0.4647 (t-100) outliers start: 51 outliers final: 34 residues processed: 162 average time/residue: 0.5594 time to fit residues: 101.7414 Evaluate side-chains 158 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 54 optimal weight: 0.0570 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 162 optimal weight: 0.0010 chunk 189 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085253 restraints weight = 72695.435| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 5.00 r_work: 0.2804 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17120 Z= 0.095 Angle : 0.499 6.828 23465 Z= 0.245 Chirality : 0.042 0.194 2775 Planarity : 0.004 0.039 2820 Dihedral : 5.841 55.326 2999 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.65 % Allowed : 12.93 % Favored : 84.42 % 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: 1.21 (0.20), residues: 1930 helix: 3.41 (0.18), residues: 745 sheet: -1.62 (0.22), residues: 485 loop : -0.19 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 328 TYR 0.014 0.001 TYR D 262 PHE 0.007 0.001 PHE A 233 TRP 0.011 0.001 TRP A 68 HIS 0.001 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00190 (17085) covalent geometry : angle 0.49281 (23365) SS BOND : bond 0.00189 ( 5) SS BOND : angle 0.75306 ( 10) hydrogen bonds : bond 0.04268 ( 860) hydrogen bonds : angle 3.93774 ( 2555) link_BETA1-4 : bond 0.00438 ( 15) link_BETA1-4 : angle 1.41142 ( 45) link_NAG-ASN : bond 0.00142 ( 15) link_NAG-ASN : angle 1.19293 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: A 223 TYR cc_start: 0.7272 (m-80) cc_final: 0.6893 (m-80) REVERT: A 291 MET cc_start: 0.5894 (tmm) cc_final: 0.5500 (tpp) REVERT: A 416 ARG cc_start: 0.6233 (mtp180) cc_final: 0.5671 (mmp-170) REVERT: A 421 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6064 (tt0) REVERT: A 456 TRP cc_start: 0.5778 (t60) cc_final: 0.4561 (t-100) REVERT: D 52 ASP cc_start: 0.7011 (t0) cc_final: 0.6359 (t0) REVERT: D 54 LYS cc_start: 0.8204 (tttm) cc_final: 0.7910 (tptm) REVERT: D 108 LYS cc_start: 0.7438 (mtmp) cc_final: 0.7069 (mtpp) REVERT: D 223 TYR cc_start: 0.6827 (m-80) cc_final: 0.6541 (m-80) REVERT: D 416 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5721 (mmp-170) REVERT: D 421 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6110 (tt0) REVERT: D 456 TRP cc_start: 0.5831 (t60) cc_final: 0.4618 (t-100) REVERT: B 41 ILE cc_start: 0.8621 (mt) cc_final: 0.8402 (mp) REVERT: B 52 ASP cc_start: 0.7025 (t0) cc_final: 0.6698 (t70) REVERT: B 60 THR cc_start: 0.8305 (p) cc_final: 0.8070 (t) REVERT: B 105 ASP cc_start: 0.8761 (t0) cc_final: 0.8261 (t0) REVERT: B 199 PHE cc_start: 0.6914 (t80) cc_final: 0.6523 (t80) REVERT: B 223 TYR cc_start: 0.7172 (m-80) cc_final: 0.6835 (m-80) REVERT: B 416 ARG cc_start: 0.6179 (mtp180) cc_final: 0.5629 (mmp-170) REVERT: B 421 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5972 (tt0) REVERT: B 456 TRP cc_start: 0.5866 (t60) cc_final: 0.4755 (t-100) REVERT: C 45 MET cc_start: 0.9177 (tpt) cc_final: 0.8872 (tpp) REVERT: C 199 PHE cc_start: 0.6778 (t80) cc_final: 0.6366 (t80) REVERT: C 421 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5679 (tt0) REVERT: C 456 TRP cc_start: 0.5926 (t60) cc_final: 0.4942 (t-100) REVERT: E 199 PHE cc_start: 0.6895 (t80) cc_final: 0.6549 (t80) REVERT: E 223 TYR cc_start: 0.7201 (m-80) cc_final: 0.6837 (m-80) REVERT: E 291 MET cc_start: 0.6910 (tpp) cc_final: 0.5810 (ttt) REVERT: E 416 ARG cc_start: 0.5952 (mtp180) cc_final: 0.5431 (mmp-170) REVERT: E 421 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: E 456 TRP cc_start: 0.5783 (t60) cc_final: 0.4678 (t-100) outliers start: 43 outliers final: 26 residues processed: 154 average time/residue: 0.5409 time to fit residues: 93.9540 Evaluate side-chains 148 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 109 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 84 optimal weight: 0.0870 chunk 156 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 311 GLN C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.084391 restraints weight = 73225.506| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.99 r_work: 0.2788 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17120 Z= 0.112 Angle : 0.510 8.618 23465 Z= 0.250 Chirality : 0.043 0.186 2775 Planarity : 0.004 0.041 2820 Dihedral : 5.715 52.470 2997 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.60 % Allowed : 13.54 % Favored : 83.87 % 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: 1.25 (0.20), residues: 1930 helix: 3.40 (0.18), residues: 745 sheet: -1.61 (0.22), residues: 490 loop : -0.09 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 328 TYR 0.021 0.001 TYR B 262 PHE 0.007 0.001 PHE D 222 TRP 0.008 0.001 TRP A 68 HIS 0.001 0.000 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00249 (17085) covalent geometry : angle 0.50408 (23365) SS BOND : bond 0.00229 ( 5) SS BOND : angle 0.77069 ( 10) hydrogen bonds : bond 0.04322 ( 860) hydrogen bonds : angle 3.92554 ( 2555) link_BETA1-4 : bond 0.00432 ( 15) link_BETA1-4 : angle 1.43103 ( 45) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 1.28323 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: A 223 TYR cc_start: 0.7252 (m-80) cc_final: 0.6884 (m-80) REVERT: A 291 MET cc_start: 0.5917 (tmm) cc_final: 0.5541 (tpp) REVERT: A 416 ARG cc_start: 0.6252 (mtp180) cc_final: 0.5686 (mmp-170) REVERT: A 421 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6090 (tt0) REVERT: A 456 TRP cc_start: 0.5806 (t60) cc_final: 0.4591 (t-100) REVERT: D 52 ASP cc_start: 0.7099 (t0) cc_final: 0.6433 (t0) REVERT: D 54 LYS cc_start: 0.8222 (tttm) cc_final: 0.7928 (tptm) REVERT: D 108 LYS cc_start: 0.7443 (mtmp) cc_final: 0.7071 (mtpp) REVERT: D 223 TYR cc_start: 0.6820 (m-80) cc_final: 0.6522 (m-80) REVERT: D 416 ARG cc_start: 0.6102 (mtp180) cc_final: 0.5727 (mmp-170) REVERT: D 421 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6109 (tt0) REVERT: D 456 TRP cc_start: 0.5824 (t60) cc_final: 0.4625 (t-100) REVERT: B 41 ILE cc_start: 0.8639 (mt) cc_final: 0.8423 (mp) REVERT: B 52 ASP cc_start: 0.7086 (t0) cc_final: 0.6753 (t70) REVERT: B 60 THR cc_start: 0.8284 (p) cc_final: 0.8037 (t) REVERT: B 105 ASP cc_start: 0.8758 (t0) cc_final: 0.8265 (t0) REVERT: B 199 PHE cc_start: 0.6907 (t80) cc_final: 0.6516 (t80) REVERT: B 223 TYR cc_start: 0.7183 (m-80) cc_final: 0.6851 (m-80) REVERT: B 250 GLU cc_start: 0.7257 (pt0) cc_final: 0.7050 (pt0) REVERT: B 311 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7056 (pp30) REVERT: B 416 ARG cc_start: 0.6089 (mtp180) cc_final: 0.5565 (mmp-170) REVERT: B 421 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5997 (tt0) REVERT: B 456 TRP cc_start: 0.5875 (t60) cc_final: 0.4748 (t-100) REVERT: C 45 MET cc_start: 0.9208 (tpt) cc_final: 0.8906 (tpp) REVERT: C 327 ASP cc_start: 0.6227 (m-30) cc_final: 0.5974 (p0) REVERT: C 421 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5697 (tt0) REVERT: C 456 TRP cc_start: 0.5872 (t60) cc_final: 0.4909 (t-100) REVERT: E 199 PHE cc_start: 0.6789 (t80) cc_final: 0.6480 (t80) REVERT: E 223 TYR cc_start: 0.7183 (m-80) cc_final: 0.6860 (m-80) REVERT: E 311 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: E 416 ARG cc_start: 0.5976 (mtp180) cc_final: 0.5453 (mmp-170) REVERT: E 421 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6185 (tt0) REVERT: E 456 TRP cc_start: 0.5785 (t60) cc_final: 0.4666 (t-100) outliers start: 42 outliers final: 30 residues processed: 154 average time/residue: 0.5535 time to fit residues: 95.8884 Evaluate side-chains 156 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.084693 restraints weight = 66042.920| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.79 r_work: 0.2802 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 17120 Z= 0.141 Angle : 0.764 59.199 23465 Z= 0.435 Chirality : 0.043 0.196 2775 Planarity : 0.005 0.123 2820 Dihedral : 5.725 52.427 2997 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.49 % Allowed : 13.54 % Favored : 83.98 % Cbeta Deviations : 0.05 % 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: 1.26 (0.20), residues: 1930 helix: 3.40 (0.18), residues: 745 sheet: -1.61 (0.22), residues: 490 loop : -0.09 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.260 0.002 TYR D 116 PHE 0.014 0.001 PHE D 233 TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00310 (17085) covalent geometry : angle 0.76047 (23365) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.75793 ( 10) hydrogen bonds : bond 0.04327 ( 860) hydrogen bonds : angle 3.92207 ( 2555) link_BETA1-4 : bond 0.00451 ( 15) link_BETA1-4 : angle 1.43286 ( 45) link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.28323 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: A 223 TYR cc_start: 0.7262 (m-80) cc_final: 0.6894 (m-80) REVERT: A 291 MET cc_start: 0.5912 (tmm) cc_final: 0.5541 (tpp) REVERT: A 416 ARG cc_start: 0.6237 (mtp180) cc_final: 0.5676 (mmp-170) REVERT: A 421 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6094 (tt0) REVERT: A 456 TRP cc_start: 0.5804 (t60) cc_final: 0.4591 (t-100) REVERT: D 52 ASP cc_start: 0.7106 (t0) cc_final: 0.6435 (t0) REVERT: D 54 LYS cc_start: 0.8225 (tttm) cc_final: 0.7931 (tptm) REVERT: D 108 LYS cc_start: 0.7460 (mtmp) cc_final: 0.7089 (mtpp) REVERT: D 223 TYR cc_start: 0.6828 (m-80) cc_final: 0.6529 (m-80) REVERT: D 416 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5724 (mmp-170) REVERT: D 421 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6106 (tt0) REVERT: D 456 TRP cc_start: 0.5840 (t60) cc_final: 0.4642 (t-100) REVERT: B 41 ILE cc_start: 0.8646 (mt) cc_final: 0.8429 (mp) REVERT: B 52 ASP cc_start: 0.7092 (t0) cc_final: 0.6762 (t70) REVERT: B 60 THR cc_start: 0.8287 (p) cc_final: 0.8041 (t) REVERT: B 105 ASP cc_start: 0.8759 (t0) cc_final: 0.8263 (t0) REVERT: B 199 PHE cc_start: 0.6936 (t80) cc_final: 0.6543 (t80) REVERT: B 223 TYR cc_start: 0.7187 (m-80) cc_final: 0.6854 (m-80) REVERT: B 250 GLU cc_start: 0.7261 (pt0) cc_final: 0.7054 (pt0) REVERT: B 311 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7199 (pp30) REVERT: B 416 ARG cc_start: 0.6087 (mtp180) cc_final: 0.5565 (mmp-170) REVERT: B 421 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5998 (tt0) REVERT: B 456 TRP cc_start: 0.5886 (t60) cc_final: 0.4755 (t-100) REVERT: C 45 MET cc_start: 0.9212 (tpt) cc_final: 0.8911 (tpp) REVERT: C 327 ASP cc_start: 0.6231 (m-30) cc_final: 0.5976 (p0) REVERT: C 421 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5693 (tt0) REVERT: C 456 TRP cc_start: 0.5892 (t60) cc_final: 0.4922 (t-100) REVERT: E 199 PHE cc_start: 0.6807 (t80) cc_final: 0.6500 (t80) REVERT: E 223 TYR cc_start: 0.7196 (m-80) cc_final: 0.6870 (m-80) REVERT: E 416 ARG cc_start: 0.6057 (mtp180) cc_final: 0.5534 (mmp-170) REVERT: E 421 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6190 (tt0) REVERT: E 456 TRP cc_start: 0.5805 (t60) cc_final: 0.4680 (t-100) outliers start: 40 outliers final: 31 residues processed: 149 average time/residue: 0.5518 time to fit residues: 92.5750 Evaluate side-chains 156 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 0.0370 chunk 129 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 137 optimal weight: 0.6980 chunk 162 optimal weight: 0.2980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084316 restraints weight = 73437.992| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.99 r_work: 0.2785 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 17120 Z= 0.141 Angle : 0.764 59.195 23465 Z= 0.435 Chirality : 0.043 0.196 2775 Planarity : 0.005 0.123 2820 Dihedral : 5.725 52.427 2997 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.38 % Allowed : 13.70 % Favored : 83.92 % Cbeta Deviations : 0.05 % 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: 1.26 (0.20), residues: 1930 helix: 3.40 (0.18), residues: 745 sheet: -1.61 (0.22), residues: 490 loop : -0.09 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.260 0.002 TYR D 116 PHE 0.014 0.001 PHE D 233 TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00310 (17085) covalent geometry : angle 0.76037 (23365) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.75789 ( 10) hydrogen bonds : bond 0.04327 ( 860) hydrogen bonds : angle 3.92206 ( 2555) link_BETA1-4 : bond 0.00450 ( 15) link_BETA1-4 : angle 1.43280 ( 45) link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.28324 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: A 223 TYR cc_start: 0.7250 (m-80) cc_final: 0.6883 (m-80) REVERT: A 291 MET cc_start: 0.5909 (tmm) cc_final: 0.5533 (tpp) REVERT: A 416 ARG cc_start: 0.6238 (mtp180) cc_final: 0.5675 (mmp-170) REVERT: A 421 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6091 (tt0) REVERT: A 456 TRP cc_start: 0.5791 (t60) cc_final: 0.4579 (t-100) REVERT: D 52 ASP cc_start: 0.7083 (t0) cc_final: 0.6416 (t0) REVERT: D 54 LYS cc_start: 0.8214 (tttm) cc_final: 0.7921 (tptm) REVERT: D 108 LYS cc_start: 0.7439 (mtmp) cc_final: 0.7071 (mtpp) REVERT: D 223 TYR cc_start: 0.6816 (m-80) cc_final: 0.6519 (m-80) REVERT: D 416 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5723 (mmp-170) REVERT: D 421 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6104 (tt0) REVERT: D 456 TRP cc_start: 0.5822 (t60) cc_final: 0.4629 (t-100) REVERT: B 41 ILE cc_start: 0.8642 (mt) cc_final: 0.8425 (mp) REVERT: B 52 ASP cc_start: 0.7074 (t0) cc_final: 0.6747 (t70) REVERT: B 60 THR cc_start: 0.8284 (p) cc_final: 0.8038 (t) REVERT: B 105 ASP cc_start: 0.8751 (t0) cc_final: 0.8257 (t0) REVERT: B 199 PHE cc_start: 0.6912 (t80) cc_final: 0.6519 (t80) REVERT: B 223 TYR cc_start: 0.7180 (m-80) cc_final: 0.6846 (m-80) REVERT: B 250 GLU cc_start: 0.7262 (pt0) cc_final: 0.7058 (pt0) REVERT: B 311 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7174 (pp30) REVERT: B 416 ARG cc_start: 0.6093 (mtp180) cc_final: 0.5568 (mmp-170) REVERT: B 421 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: B 456 TRP cc_start: 0.5877 (t60) cc_final: 0.4748 (t-100) REVERT: C 45 MET cc_start: 0.9205 (tpt) cc_final: 0.8904 (tpp) REVERT: C 327 ASP cc_start: 0.6225 (m-30) cc_final: 0.5975 (p0) REVERT: C 421 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5692 (tt0) REVERT: C 456 TRP cc_start: 0.5879 (t60) cc_final: 0.4914 (t-100) REVERT: E 199 PHE cc_start: 0.6783 (t80) cc_final: 0.6476 (t80) REVERT: E 223 TYR cc_start: 0.7189 (m-80) cc_final: 0.6864 (m-80) REVERT: E 416 ARG cc_start: 0.6050 (mtp180) cc_final: 0.5527 (mmp-170) REVERT: E 421 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6186 (tt0) REVERT: E 456 TRP cc_start: 0.5787 (t60) cc_final: 0.4668 (t-100) outliers start: 38 outliers final: 31 residues processed: 147 average time/residue: 0.5625 time to fit residues: 92.6706 Evaluate side-chains 156 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 124 optimal weight: 0.0040 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.084017 restraints weight = 83205.921| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 5.23 r_work: 0.2772 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 17120 Z= 0.140 Angle : 0.762 59.116 23465 Z= 0.433 Chirality : 0.043 0.198 2775 Planarity : 0.005 0.122 2820 Dihedral : 5.724 52.428 2997 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.38 % Allowed : 13.70 % Favored : 83.92 % Cbeta Deviations : 0.05 % 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: 1.26 (0.20), residues: 1930 helix: 3.40 (0.18), residues: 745 sheet: -1.61 (0.22), residues: 490 loop : -0.09 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.257 0.002 TYR D 116 PHE 0.014 0.001 PHE D 233 TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS E 503 Details of bonding type rmsd covalent geometry : bond 0.00308 (17085) covalent geometry : angle 0.75861 (23365) SS BOND : bond 0.00214 ( 5) SS BOND : angle 0.75721 ( 10) hydrogen bonds : bond 0.04325 ( 860) hydrogen bonds : angle 3.92196 ( 2555) link_BETA1-4 : bond 0.00430 ( 15) link_BETA1-4 : angle 1.43256 ( 45) link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.28347 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5309.19 seconds wall clock time: 90 minutes 59.05 seconds (5459.05 seconds total)