Starting phenix.real_space_refine on Sat Sep 12 15:23:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y1z_10673/09_2026/6y1z_10673.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y1z_10673/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6y1z_10673/09_2026/6y1z_10673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y1z_10673/09_2026/6y1z_10673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y1z_10673/09_2026/6y1z_10673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y1z_10673/09_2026/6y1z_10673.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6y1z_10673/09_2026/6y1z_10673.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y1z_10673/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 6.46, per 1000 atoms: 0.39 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: 1.37 Conformation dependent library (CDL) restraints added in 1.4 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: 0.43 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: 2.71 Time building geometry restraints manager: 1.93 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 - 17.35: 9385 17.35 - 34.70: 400 34.70 - 52.05: 130 52.05 - 69.40: 25 69.40 - 86.75: 15 Dihedral angle restraints: 9955 sinusoidal: 4160 harmonic: 5795 Sorted by residual: dihedral pdb=" CB GLU E 172 " pdb=" CG GLU E 172 " pdb=" CD GLU E 172 " pdb=" OE1 GLU E 172 " ideal model delta sinusoidal sigma weight residual 0.00 86.75 -86.75 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU B 172 " pdb=" CG GLU B 172 " pdb=" CD GLU B 172 " pdb=" OE1 GLU B 172 " ideal model delta sinusoidal sigma weight residual 0.00 86.74 -86.74 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 172 " pdb=" CG GLU A 172 " pdb=" CD GLU A 172 " pdb=" OE1 GLU A 172 " ideal model delta sinusoidal sigma weight residual 0.00 86.73 -86.73 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 9952 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: 0.04 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.960 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 11.877 86.748 6170 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/Z covalent geometry : bond 0.00320 / 0.17 (17085) covalent geometry : angle 0.57667 / 0.29 (23365) SS BOND : bond 0.00083 / 0.04 ( 5) SS BOND : angle 0.32277 / 0.18 ( 10) hydrogen bonds : bond 0.13942 / 9.21 ( 860) hydrogen bonds : angle 5.68966 / 3.98 ( 2555) link_BETA1-4 : bond 0.00481 / 0.27 ( 15) link_BETA1-4 : angle 1.22262 / 0.74 ( 45) link_NAG-ASN : bond 0.00067 / 0.03 ( 15) link_NAG-ASN : angle 1.16985 / 0.78 ( 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 : 0.917 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: 0.5638 time to fit residues: 150.3715 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 : 0.693 ------------------------------------------------------------------------------- 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... 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 = 0.3469 r_free = 0.3469 target = 0.119399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.084453 restraints weight = 65741.014| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.65 r_work: 0.2775 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17120 Z= 0.106 Angle : 0.539 8.332 23465 Z= 0.267 Chirality : 0.043 0.137 2775 Planarity : 0.004 0.034 2820 Dihedral : 6.228 66.755 2384 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.60 % Allowed : 10.39 % Favored : 87.02 % 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: -2.35 (0.20), residues: 485 loop : -1.37 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.013 0.001 TYR D 64 PHE 0.008 0.001 PHE D 222 TRP 0.010 0.001 TRP E 68 HIS 0.001 0.000 HIS E 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (17085) covalent geometry : angle 0.53562 / 0.27 (23365) SS BOND : bond 0.00195 / 0.10 ( 5) SS BOND : angle 1.03746 / 0.64 ( 10) hydrogen bonds : bond 0.04816 / 3.11 ( 860) hydrogen bonds : angle 4.47231 / 3.09 ( 2555) link_BETA1-4 : bond 0.00408 / 0.23 ( 15) link_BETA1-4 : angle 1.18234 / 0.72 ( 45) link_NAG-ASN : bond 0.00137 / 0.07 ( 15) link_NAG-ASN : angle 1.04738 / 0.69 ( 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 : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8492 (mt) cc_final: 0.8261 (mp) REVERT: A 52 ASP cc_start: 0.6756 (t0) cc_final: 0.6174 (t0) REVERT: A 54 LYS cc_start: 0.8152 (tttm) cc_final: 0.7940 (tttm) REVERT: A 105 ASP cc_start: 0.8635 (t0) cc_final: 0.8088 (t0) REVERT: A 108 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7159 (mtpp) REVERT: A 144 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: A 210 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8359 (tpp) REVERT: A 223 TYR cc_start: 0.7235 (m-80) cc_final: 0.6936 (m-80) REVERT: A 291 MET cc_start: 0.5905 (tmm) cc_final: 0.5625 (tpp) REVERT: A 421 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6057 (tt0) REVERT: A 456 TRP cc_start: 0.5781 (t60) cc_final: 0.4661 (t-100) REVERT: D 52 ASP cc_start: 0.6931 (t0) cc_final: 0.6397 (t0) REVERT: D 54 LYS cc_start: 0.8354 (tttm) cc_final: 0.8116 (tptm) REVERT: D 144 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: D 223 TYR cc_start: 0.6774 (m-80) cc_final: 0.6514 (m-80) REVERT: D 416 ARG cc_start: 0.6056 (mtp180) cc_final: 0.5599 (mmp-170) REVERT: D 421 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6026 (tt0) REVERT: D 456 TRP cc_start: 0.5799 (t60) cc_final: 0.4726 (t-100) REVERT: B 52 ASP cc_start: 0.7067 (t0) cc_final: 0.6823 (t70) REVERT: B 105 ASP cc_start: 0.8758 (t0) cc_final: 0.8382 (t0) REVERT: B 199 PHE cc_start: 0.6634 (t80) cc_final: 0.6305 (t80) REVERT: B 291 MET cc_start: 0.7094 (ttp) cc_final: 0.6252 (ttp) REVERT: B 416 ARG cc_start: 0.6134 (mtp180) cc_final: 0.5640 (mmp-170) REVERT: B 421 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5915 (tt0) REVERT: B 456 TRP cc_start: 0.5734 (t60) cc_final: 0.4714 (t-100) REVERT: C 210 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8296 (tpp) REVERT: C 421 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5735 (tp30) REVERT: C 456 TRP cc_start: 0.5925 (t60) cc_final: 0.4963 (t-100) REVERT: E 35 LYS cc_start: 0.7536 (mmtt) cc_final: 0.6766 (tttp) REVERT: E 199 PHE cc_start: 0.6852 (t80) cc_final: 0.6511 (t80) REVERT: E 223 TYR cc_start: 0.7090 (m-80) cc_final: 0.6714 (m-80) REVERT: E 416 ARG cc_start: 0.5837 (mtp180) cc_final: 0.5343 (mmp-170) REVERT: E 421 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6057 (tt0) REVERT: E 456 TRP cc_start: 0.5629 (t60) cc_final: 0.4544 (t-100) outliers start: 42 outliers final: 19 residues processed: 164 average time/residue: 0.4881 time to fit residues: 91.1213 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 : 0.698 ------------------------------------------------------------------------------- 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: 5.9990 chunk 36 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 55 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.082133 restraints weight = 62036.103| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.51 r_work: 0.2743 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 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 = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17120 Z= 0.154 Angle : 0.547 7.370 23465 Z= 0.270 Chirality : 0.044 0.140 2775 Planarity : 0.004 0.040 2820 Dihedral : 6.269 65.573 2381 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.15 % Allowed : 10.44 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1930 helix: 2.74 (0.18), residues: 745 sheet: -2.05 (0.21), residues: 490 loop : -0.95 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 328 TYR 0.015 0.001 TYR C 64 PHE 0.009 0.001 PHE A 222 TRP 0.012 0.001 TRP B 320 HIS 0.002 0.000 HIS C 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (17085) covalent geometry : angle 0.54143 / 0.27 (23365) SS BOND : bond 0.00334 / 0.17 ( 5) SS BOND : angle 1.21284 / 0.73 ( 10) hydrogen bonds : bond 0.04952 / 3.18 ( 860) hydrogen bonds : angle 4.25163 / 2.94 ( 2555) link_BETA1-4 : bond 0.00480 / 0.27 ( 15) link_BETA1-4 : angle 1.24887 / 0.77 ( 45) link_NAG-ASN : bond 0.00169 / 0.09 ( 15) link_NAG-ASN : angle 1.40772 / 0.93 ( 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 172 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8514 (mt) cc_final: 0.8269 (mp) REVERT: A 105 ASP cc_start: 0.8695 (t0) cc_final: 0.8052 (t0) REVERT: A 144 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: A 223 TYR cc_start: 0.7294 (m-80) cc_final: 0.6966 (m-80) REVERT: A 416 ARG cc_start: 0.6266 (mtp180) cc_final: 0.5703 (mmp-170) REVERT: A 421 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: A 456 TRP cc_start: 0.5807 (t60) cc_final: 0.4629 (t-100) REVERT: D 52 ASP cc_start: 0.7007 (t0) cc_final: 0.6465 (t0) REVERT: D 54 LYS cc_start: 0.8336 (tttm) cc_final: 0.8084 (tptm) REVERT: D 108 LYS cc_start: 0.7647 (mtmp) cc_final: 0.7281 (mtpp) REVERT: D 223 TYR cc_start: 0.6827 (m-80) cc_final: 0.6548 (m-80) REVERT: D 250 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6978 (mt-10) REVERT: D 416 ARG cc_start: 0.6165 (mtp180) cc_final: 0.5722 (mmp-170) REVERT: D 421 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6065 (tt0) REVERT: D 456 TRP cc_start: 0.5953 (t60) cc_final: 0.4781 (t-100) REVERT: B 52 ASP cc_start: 0.7036 (t0) cc_final: 0.6777 (t70) REVERT: B 60 THR cc_start: 0.8426 (p) cc_final: 0.8051 (t) REVERT: B 105 ASP cc_start: 0.8772 (t0) cc_final: 0.8321 (t0) REVERT: B 199 PHE cc_start: 0.6670 (t80) cc_final: 0.6199 (t80) REVERT: B 223 TYR cc_start: 0.7132 (m-80) cc_final: 0.6755 (m-80) REVERT: B 291 MET cc_start: 0.7069 (ttp) cc_final: 0.6312 (ttp) REVERT: B 311 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: B 416 ARG cc_start: 0.6166 (mtp180) cc_final: 0.5568 (mmp-170) REVERT: B 421 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5954 (tt0) REVERT: B 456 TRP cc_start: 0.5850 (t60) cc_final: 0.4801 (t-100) REVERT: C 103 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: C 311 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: C 421 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5672 (tp30) REVERT: C 456 TRP cc_start: 0.5961 (t60) cc_final: 0.4985 (t-100) REVERT: E 223 TYR cc_start: 0.7209 (m-80) cc_final: 0.6879 (m-80) REVERT: E 291 MET cc_start: 0.7070 (tpp) cc_final: 0.6458 (ttp) REVERT: E 416 ARG cc_start: 0.5883 (mtp180) cc_final: 0.5354 (mmp-170) REVERT: E 421 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6086 (tt0) REVERT: E 456 TRP cc_start: 0.5656 (t60) cc_final: 0.4543 (t-100) outliers start: 52 outliers final: 27 residues processed: 161 average time/residue: 0.5562 time to fit residues: 101.0937 Evaluate side-chains 151 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 A residue 453 VAL Chi-restraints excluded: chain D residue 41 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 D residue 453 VAL 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 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 103 PHE 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 296 ILE Chi-restraints excluded: chain C residue 311 GLN 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 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: 3.9990 chunk 166 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 22 ASN C 22 ASN C 111 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 = 0.3423 r_free = 0.3423 target = 0.115617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.080452 restraints weight = 75941.380| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.87 r_work: 0.2705 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17120 Z= 0.185 Angle : 0.563 7.106 23465 Z= 0.278 Chirality : 0.045 0.142 2775 Planarity : 0.004 0.044 2820 Dihedral : 6.309 63.958 2379 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.54 % Allowed : 10.22 % Favored : 86.24 % 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: 0.48 (0.20), residues: 1930 helix: 2.84 (0.18), residues: 745 sheet: -1.92 (0.21), residues: 490 loop : -0.70 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 328 TYR 0.019 0.001 TYR C 64 PHE 0.011 0.001 PHE A 222 TRP 0.015 0.001 TRP B 320 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (17085) covalent geometry : angle 0.55703 / 0.28 (23365) SS BOND : bond 0.00321 / 0.16 ( 5) SS BOND : angle 1.12840 / 0.67 ( 10) hydrogen bonds : bond 0.05132 / 3.29 ( 860) hydrogen bonds : angle 4.22245 / 2.92 ( 2555) link_BETA1-4 : bond 0.00368 / 0.21 ( 15) link_BETA1-4 : angle 1.29378 / 0.79 ( 45) link_NAG-ASN : bond 0.00204 / 0.12 ( 15) link_NAG-ASN : angle 1.46790 / 0.96 ( 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 180 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8524 (mt) cc_final: 0.8288 (mp) REVERT: A 108 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7226 (mtpp) REVERT: A 144 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: A 223 TYR cc_start: 0.7363 (m-80) cc_final: 0.7058 (m-80) REVERT: A 416 ARG cc_start: 0.6193 (mtp180) cc_final: 0.5623 (mmp-170) REVERT: A 421 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6101 (tt0) REVERT: A 456 TRP cc_start: 0.5797 (t60) cc_final: 0.4598 (t-100) REVERT: D 52 ASP cc_start: 0.7039 (t0) cc_final: 0.6418 (t0) REVERT: D 54 LYS cc_start: 0.8472 (tttm) cc_final: 0.8260 (tptm) REVERT: D 108 LYS cc_start: 0.7605 (mtmp) cc_final: 0.7232 (mtpp) REVERT: D 223 TYR cc_start: 0.6860 (m-80) cc_final: 0.6582 (m-80) REVERT: D 416 ARG cc_start: 0.6063 (mtp180) cc_final: 0.5722 (mmp-170) REVERT: D 421 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6162 (tt0) REVERT: D 456 TRP cc_start: 0.5881 (t60) cc_final: 0.4670 (t-100) REVERT: B 52 ASP cc_start: 0.7105 (t0) cc_final: 0.6834 (t70) REVERT: B 105 ASP cc_start: 0.8802 (t0) cc_final: 0.8314 (t0) REVERT: B 199 PHE cc_start: 0.6776 (t80) cc_final: 0.6376 (t80) REVERT: B 223 TYR cc_start: 0.7100 (m-80) cc_final: 0.6755 (m-80) REVERT: B 291 MET cc_start: 0.7104 (ttp) cc_final: 0.6335 (ttp) REVERT: B 311 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: B 416 ARG cc_start: 0.5964 (mtp180) cc_final: 0.5442 (mmp-170) REVERT: B 421 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5989 (tt0) REVERT: B 456 TRP cc_start: 0.5952 (t60) cc_final: 0.4808 (t-100) REVERT: C 291 MET cc_start: 0.6476 (tmm) cc_final: 0.6199 (tpt) REVERT: C 416 ARG cc_start: 0.5997 (mtp180) cc_final: 0.5502 (mmp-170) REVERT: C 421 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5719 (tp30) REVERT: C 456 TRP cc_start: 0.5842 (t60) cc_final: 0.4811 (t-100) REVERT: E 223 TYR cc_start: 0.7226 (m-80) cc_final: 0.6851 (m-80) REVERT: E 311 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: E 416 ARG cc_start: 0.6019 (mtp180) cc_final: 0.5499 (mmp-170) REVERT: E 421 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6128 (tt0) REVERT: E 456 TRP cc_start: 0.5814 (t60) cc_final: 0.4664 (t-100) outliers start: 59 outliers final: 36 residues processed: 169 average time/residue: 0.5155 time to fit residues: 98.7786 Evaluate side-chains 157 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 453 VAL 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 240 VAL 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 B residue 453 VAL 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 C residue 453 VAL 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 311 GLN Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 184 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN D 22 ASN D 50 ASN B 50 ASN C 22 ASN C 50 ASN E 50 ASN E 404 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.083532 restraints weight = 73518.987| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.86 r_work: 0.2762 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17120 Z= 0.102 Angle : 0.500 6.750 23465 Z= 0.247 Chirality : 0.043 0.141 2775 Planarity : 0.004 0.039 2820 Dihedral : 6.084 60.237 2379 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 12.04 % Favored : 85.30 % 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: 0.94 (0.20), residues: 1930 helix: 3.24 (0.18), residues: 745 sheet: -1.76 (0.22), residues: 485 loop : -0.41 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 328 TYR 0.016 0.001 TYR D 262 PHE 0.008 0.001 PHE E 254 TRP 0.020 0.001 TRP B 320 HIS 0.001 0.000 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (17085) covalent geometry : angle 0.49580 / 0.25 (23365) SS BOND : bond 0.00239 / 0.12 ( 5) SS BOND : angle 0.87026 / 0.53 ( 10) hydrogen bonds : bond 0.04434 / 2.84 ( 860) hydrogen bonds : angle 4.03670 / 2.77 ( 2555) link_BETA1-4 : bond 0.00451 / 0.26 ( 15) link_BETA1-4 : angle 1.19872 / 0.73 ( 45) link_NAG-ASN : bond 0.00171 / 0.09 ( 15) link_NAG-ASN : angle 1.14599 / 0.73 ( 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 172 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8438 (mt) cc_final: 0.8220 (mp) REVERT: A 144 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: A 223 TYR cc_start: 0.7183 (m-80) cc_final: 0.6827 (m-80) REVERT: A 291 MET cc_start: 0.6237 (tmm) cc_final: 0.5983 (tpp) REVERT: A 416 ARG cc_start: 0.6217 (mtp180) cc_final: 0.5644 (mmp-170) REVERT: A 421 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6021 (tt0) REVERT: A 456 TRP cc_start: 0.5727 (t60) cc_final: 0.4549 (t-100) REVERT: D 52 ASP cc_start: 0.6936 (t0) cc_final: 0.6347 (t0) REVERT: D 54 LYS cc_start: 0.8447 (tttm) cc_final: 0.8231 (tptm) REVERT: D 108 LYS cc_start: 0.7418 (mtmp) cc_final: 0.7044 (mtpp) REVERT: D 223 TYR cc_start: 0.6694 (m-80) cc_final: 0.6381 (m-80) REVERT: D 416 ARG cc_start: 0.6052 (mtp180) cc_final: 0.5645 (mmp-170) REVERT: D 421 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6043 (tt0) REVERT: D 456 TRP cc_start: 0.5666 (t60) cc_final: 0.4462 (t-100) REVERT: B 41 ILE cc_start: 0.8589 (mt) cc_final: 0.8386 (mp) REVERT: B 52 ASP cc_start: 0.6963 (t0) cc_final: 0.6660 (t70) REVERT: B 60 THR cc_start: 0.8251 (p) cc_final: 0.8024 (t) REVERT: B 105 ASP cc_start: 0.8758 (t0) cc_final: 0.8285 (t0) REVERT: B 199 PHE cc_start: 0.6860 (t80) cc_final: 0.6504 (t80) REVERT: B 223 TYR cc_start: 0.7064 (m-80) cc_final: 0.6753 (m-80) REVERT: B 291 MET cc_start: 0.6930 (ttp) cc_final: 0.6101 (ttp) REVERT: B 416 ARG cc_start: 0.6032 (mtp180) cc_final: 0.5489 (mmp-170) REVERT: B 421 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5918 (tt0) REVERT: B 456 TRP cc_start: 0.5889 (t60) cc_final: 0.4788 (t-100) REVERT: C 41 ILE cc_start: 0.8367 (mt) cc_final: 0.7999 (pt) REVERT: C 45 MET cc_start: 0.9083 (tpt) cc_final: 0.8803 (tpp) REVERT: C 108 LYS cc_start: 0.7344 (mtmp) cc_final: 0.7136 (mtpp) REVERT: C 199 PHE cc_start: 0.6802 (t80) cc_final: 0.6506 (t80) REVERT: C 421 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5567 (tt0) REVERT: C 456 TRP cc_start: 0.5858 (t60) cc_final: 0.4850 (t-100) REVERT: E 199 PHE cc_start: 0.6883 (t80) cc_final: 0.6536 (t80) REVERT: E 223 TYR cc_start: 0.7060 (m-80) cc_final: 0.6742 (m-80) REVERT: E 416 ARG cc_start: 0.5888 (mtp180) cc_final: 0.5372 (mmp-170) REVERT: E 421 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6075 (tt0) REVERT: E 456 TRP cc_start: 0.5796 (t60) cc_final: 0.4671 (t-100) outliers start: 43 outliers final: 25 residues processed: 162 average time/residue: 0.5322 time to fit residues: 97.9122 Evaluate side-chains 154 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 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 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 421 GLU 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 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 421 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 83 optimal weight: 0.0070 chunk 124 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 22 ASN C 22 ASN C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.083190 restraints weight = 71774.462| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.82 r_work: 0.2768 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17120 Z= 0.110 Angle : 0.507 8.545 23465 Z= 0.248 Chirality : 0.043 0.133 2775 Planarity : 0.004 0.039 2820 Dihedral : 6.026 58.070 2379 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.71 % Allowed : 12.93 % Favored : 84.36 % 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: 1.10 (0.20), residues: 1930 helix: 3.31 (0.17), residues: 745 sheet: -1.69 (0.22), residues: 490 loop : -0.23 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.013 0.001 TYR E 64 PHE 0.007 0.001 PHE A 233 TRP 0.018 0.001 TRP B 320 HIS 0.001 0.000 HIS E 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (17085) covalent geometry : angle 0.50227 / 0.25 (23365) SS BOND : bond 0.00224 / 0.11 ( 5) SS BOND : angle 0.85652 / 0.52 ( 10) hydrogen bonds : bond 0.04429 / 2.84 ( 860) hydrogen bonds : angle 3.98423 / 2.74 ( 2555) link_BETA1-4 : bond 0.00418 / 0.24 ( 15) link_BETA1-4 : angle 1.23612 / 0.76 ( 45) link_NAG-ASN : bond 0.00131 / 0.07 ( 15) link_NAG-ASN : angle 1.22472 / 0.78 ( 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 170 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8449 (mt) cc_final: 0.8235 (mp) REVERT: A 223 TYR cc_start: 0.7199 (m-80) cc_final: 0.6792 (m-80) REVERT: A 291 MET cc_start: 0.6268 (tmm) cc_final: 0.6008 (tpp) REVERT: A 416 ARG cc_start: 0.6203 (mtp180) cc_final: 0.5634 (mmp-170) REVERT: A 421 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6026 (tt0) REVERT: A 456 TRP cc_start: 0.5669 (t60) cc_final: 0.4487 (t-100) REVERT: D 52 ASP cc_start: 0.6963 (t0) cc_final: 0.6374 (t0) REVERT: D 54 LYS cc_start: 0.8447 (tttm) cc_final: 0.8231 (tptm) REVERT: D 108 LYS cc_start: 0.7422 (mtmp) cc_final: 0.7044 (mtpp) REVERT: D 223 TYR cc_start: 0.6724 (m-80) cc_final: 0.6453 (m-80) REVERT: D 416 ARG cc_start: 0.6005 (mtp180) cc_final: 0.5654 (mmp-170) REVERT: D 421 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6036 (tt0) REVERT: D 456 TRP cc_start: 0.5728 (t60) cc_final: 0.4509 (t-100) REVERT: B 41 ILE cc_start: 0.8570 (mt) cc_final: 0.8361 (mp) REVERT: B 52 ASP cc_start: 0.7023 (t0) cc_final: 0.6714 (t70) REVERT: B 60 THR cc_start: 0.8242 (p) cc_final: 0.8031 (t) REVERT: B 105 ASP cc_start: 0.8684 (t0) cc_final: 0.8191 (t0) REVERT: B 199 PHE cc_start: 0.6854 (t80) cc_final: 0.6503 (t80) REVERT: B 223 TYR cc_start: 0.7086 (m-80) cc_final: 0.6692 (m-80) REVERT: B 250 GLU cc_start: 0.7045 (pt0) cc_final: 0.6765 (pt0) REVERT: B 416 ARG cc_start: 0.6032 (mtp180) cc_final: 0.5484 (mmp-170) REVERT: B 421 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5907 (tt0) REVERT: B 456 TRP cc_start: 0.5866 (t60) cc_final: 0.4759 (t-100) REVERT: C 45 MET cc_start: 0.9165 (tpt) cc_final: 0.8867 (tpp) REVERT: C 108 LYS cc_start: 0.7334 (mtmp) cc_final: 0.7120 (mtpp) REVERT: C 421 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5566 (tt0) REVERT: C 456 TRP cc_start: 0.5865 (t60) cc_final: 0.4851 (t-100) REVERT: E 199 PHE cc_start: 0.6774 (t80) cc_final: 0.6431 (t80) REVERT: E 223 TYR cc_start: 0.7096 (m-80) cc_final: 0.6790 (m-80) REVERT: E 291 MET cc_start: 0.6979 (tpp) cc_final: 0.5783 (ttt) REVERT: E 416 ARG cc_start: 0.5881 (mtp180) cc_final: 0.5367 (mmp-170) REVERT: E 421 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6108 (tt0) REVERT: E 456 TRP cc_start: 0.5719 (t60) cc_final: 0.4586 (t-100) outliers start: 44 outliers final: 31 residues processed: 162 average time/residue: 0.5517 time to fit residues: 100.9642 Evaluate side-chains 156 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 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 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 421 GLU Chi-restraints excluded: chain B residue 450 ILE 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 269 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain E residue 44 ILE 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 421 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 54 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN D 22 ASN C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.083281 restraints weight = 72006.003| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.83 r_work: 0.2758 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 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 = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2018 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= 0.114 Angle : 0.512 8.994 23465 Z= 0.251 Chirality : 0.043 0.207 2775 Planarity : 0.004 0.039 2820 Dihedral : 5.959 55.970 2377 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.54 % Allowed : 13.37 % Favored : 84.09 % 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: 1.17 (0.20), residues: 1930 helix: 3.35 (0.17), residues: 745 sheet: -1.64 (0.22), residues: 490 loop : -0.16 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 328 TYR 0.017 0.001 TYR D 116 PHE 0.008 0.001 PHE A 144 TRP 0.015 0.001 TRP B 320 HIS 0.001 0.000 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (17085) covalent geometry : angle 0.50738 / 0.25 (23365) SS BOND : bond 0.00218 / 0.11 ( 5) SS BOND : angle 0.82391 / 0.50 ( 10) hydrogen bonds : bond 0.04397 / 2.82 ( 860) hydrogen bonds : angle 3.97450 / 2.73 ( 2555) link_BETA1-4 : bond 0.00427 / 0.24 ( 15) link_BETA1-4 : angle 1.24290 / 0.76 ( 45) link_NAG-ASN : bond 0.00130 / 0.07 ( 15) link_NAG-ASN : angle 1.23736 / 0.79 ( 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: 41 poor density : 123 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8492 (mt) cc_final: 0.8271 (mp) REVERT: A 199 PHE cc_start: 0.7043 (t80) cc_final: 0.6783 (t80) REVERT: A 223 TYR cc_start: 0.7232 (m-80) cc_final: 0.6827 (m-80) REVERT: A 291 MET cc_start: 0.6327 (tmm) cc_final: 0.6048 (tpp) REVERT: A 311 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6906 (pp30) REVERT: A 416 ARG cc_start: 0.6203 (mtp180) cc_final: 0.5635 (mmp-170) REVERT: A 421 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6018 (tt0) REVERT: A 456 TRP cc_start: 0.5673 (t60) cc_final: 0.4488 (t-100) REVERT: D 52 ASP cc_start: 0.6976 (t0) cc_final: 0.6384 (t0) REVERT: D 54 LYS cc_start: 0.8448 (tttm) cc_final: 0.8231 (tptm) REVERT: D 223 TYR cc_start: 0.6726 (m-80) cc_final: 0.6452 (m-80) REVERT: D 416 ARG cc_start: 0.6042 (mtp180) cc_final: 0.5694 (mmp-170) REVERT: D 421 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6114 (tt0) REVERT: D 456 TRP cc_start: 0.5713 (t60) cc_final: 0.4493 (t-100) REVERT: B 41 ILE cc_start: 0.8573 (mt) cc_final: 0.8362 (mp) REVERT: B 52 ASP cc_start: 0.7014 (t0) cc_final: 0.6705 (t70) REVERT: B 60 THR cc_start: 0.8245 (p) cc_final: 0.8019 (t) REVERT: B 105 ASP cc_start: 0.8678 (t0) cc_final: 0.8180 (t0) REVERT: B 199 PHE cc_start: 0.6835 (t80) cc_final: 0.6495 (t80) REVERT: B 223 TYR cc_start: 0.7078 (m-80) cc_final: 0.6688 (m-80) REVERT: B 250 GLU cc_start: 0.7151 (pt0) cc_final: 0.6950 (pt0) REVERT: B 291 MET cc_start: 0.6854 (tpp) cc_final: 0.5528 (ttt) REVERT: B 416 ARG cc_start: 0.6039 (mtp180) cc_final: 0.5495 (mmp-170) REVERT: B 421 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5921 (tt0) REVERT: B 456 TRP cc_start: 0.5867 (t60) cc_final: 0.4760 (t-100) REVERT: C 41 ILE cc_start: 0.8483 (mt) cc_final: 0.8106 (pt) REVERT: C 45 MET cc_start: 0.9158 (tpt) cc_final: 0.8871 (tpp) REVERT: C 108 LYS cc_start: 0.7324 (mtmp) cc_final: 0.7104 (mtpp) REVERT: C 421 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5572 (tt0) REVERT: C 456 TRP cc_start: 0.5805 (t60) cc_final: 0.4814 (t-100) REVERT: E 199 PHE cc_start: 0.6778 (t80) cc_final: 0.6442 (t80) REVERT: E 223 TYR cc_start: 0.7141 (m-80) cc_final: 0.6814 (m-80) REVERT: E 416 ARG cc_start: 0.5963 (mtp180) cc_final: 0.5469 (mmp-170) REVERT: E 421 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6129 (tt0) REVERT: E 456 TRP cc_start: 0.5695 (t60) cc_final: 0.4568 (t-100) outliers start: 41 outliers final: 29 residues processed: 157 average time/residue: 0.5419 time to fit residues: 96.4085 Evaluate side-chains 154 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE 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 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 421 GLU Chi-restraints excluded: chain B residue 450 ILE 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 269 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 421 GLU 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 421 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 109 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 126 optimal weight: 0.4980 chunk 84 optimal weight: 0.0970 chunk 156 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN D 22 ASN C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.084353 restraints weight = 72803.710| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.87 r_work: 0.2776 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 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 = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17120 Z= 0.098 Angle : 0.509 11.030 23465 Z= 0.248 Chirality : 0.043 0.267 2775 Planarity : 0.004 0.038 2820 Dihedral : 5.880 53.287 2377 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.49 % Allowed : 13.76 % Favored : 83.76 % 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: 1.26 (0.20), residues: 1930 helix: 3.41 (0.18), residues: 745 sheet: -1.59 (0.22), residues: 485 loop : -0.12 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.033 0.001 TYR D 262 PHE 0.008 0.001 PHE D 233 TRP 0.015 0.001 TRP B 320 HIS 0.001 0.000 HIS E 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (17085) covalent geometry : angle 0.50435 / 0.25 (23365) SS BOND : bond 0.00191 / 0.09 ( 5) SS BOND : angle 0.75735 / 0.46 ( 10) hydrogen bonds : bond 0.04208 / 2.70 ( 860) hydrogen bonds : angle 3.91594 / 2.69 ( 2555) link_BETA1-4 : bond 0.00433 / 0.24 ( 15) link_BETA1-4 : angle 1.21682 / 0.75 ( 45) link_NAG-ASN : bond 0.00136 / 0.07 ( 15) link_NAG-ASN : angle 1.15753 / 0.73 ( 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 171 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8435 (mt) cc_final: 0.8221 (mp) REVERT: A 199 PHE cc_start: 0.7022 (t80) cc_final: 0.6745 (t80) REVERT: A 223 TYR cc_start: 0.7167 (m-80) cc_final: 0.6762 (m-80) REVERT: A 291 MET cc_start: 0.6355 (tmm) cc_final: 0.6024 (tpp) REVERT: A 311 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6773 (pp30) REVERT: A 416 ARG cc_start: 0.6147 (mtp180) cc_final: 0.5588 (mmp-170) REVERT: A 421 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6000 (tt0) REVERT: A 456 TRP cc_start: 0.5691 (t60) cc_final: 0.4492 (t-100) REVERT: D 52 ASP cc_start: 0.6958 (t0) cc_final: 0.6352 (t0) REVERT: D 54 LYS cc_start: 0.8182 (tttm) cc_final: 0.7895 (tptm) REVERT: D 223 TYR cc_start: 0.6755 (m-80) cc_final: 0.6446 (m-80) REVERT: D 416 ARG cc_start: 0.6007 (mtp180) cc_final: 0.5646 (mmp-170) REVERT: D 421 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6024 (tt0) REVERT: D 456 TRP cc_start: 0.5739 (t60) cc_final: 0.4548 (t-100) REVERT: B 41 ILE cc_start: 0.8584 (mt) cc_final: 0.8379 (mp) REVERT: B 52 ASP cc_start: 0.6987 (t0) cc_final: 0.6679 (t70) REVERT: B 60 THR cc_start: 0.8224 (p) cc_final: 0.8021 (t) REVERT: B 105 ASP cc_start: 0.8684 (t0) cc_final: 0.8185 (t0) REVERT: B 199 PHE cc_start: 0.6872 (t80) cc_final: 0.6514 (t80) REVERT: B 223 TYR cc_start: 0.7199 (m-80) cc_final: 0.6862 (m-80) REVERT: B 416 ARG cc_start: 0.6008 (mtp180) cc_final: 0.5478 (mmp-170) REVERT: B 421 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5901 (tt0) REVERT: B 456 TRP cc_start: 0.5809 (t60) cc_final: 0.4706 (t-100) REVERT: C 41 ILE cc_start: 0.8480 (mt) cc_final: 0.8103 (pt) REVERT: C 45 MET cc_start: 0.9149 (tpt) cc_final: 0.8855 (tpp) REVERT: C 108 LYS cc_start: 0.7292 (mtmp) cc_final: 0.7054 (mtpp) REVERT: C 421 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5608 (tt0) REVERT: C 456 TRP cc_start: 0.5833 (t60) cc_final: 0.4866 (t-100) REVERT: E 199 PHE cc_start: 0.6876 (t80) cc_final: 0.6526 (t80) REVERT: E 223 TYR cc_start: 0.7117 (m-80) cc_final: 0.6812 (m-80) REVERT: E 416 ARG cc_start: 0.5940 (mtp180) cc_final: 0.5434 (mmp-170) REVERT: E 421 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6124 (tt0) REVERT: E 456 TRP cc_start: 0.5694 (t60) cc_final: 0.4607 (t-100) outliers start: 40 outliers final: 24 residues processed: 162 average time/residue: 0.5291 time to fit residues: 97.6015 Evaluate side-chains 157 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 269 VAL 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 296 ILE Chi-restraints excluded: chain B residue 421 GLU 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 421 GLU 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 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3473 r_free = 0.3473 target = 0.119621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.084513 restraints weight = 65205.301| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.65 r_work: 0.2785 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17120 Z= 0.107 Angle : 0.526 10.429 23465 Z= 0.252 Chirality : 0.043 0.163 2775 Planarity : 0.004 0.039 2820 Dihedral : 5.639 51.183 2371 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.15 % Allowed : 14.36 % Favored : 83.48 % 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: 1.28 (0.20), residues: 1930 helix: 3.39 (0.18), residues: 745 sheet: -1.56 (0.22), residues: 485 loop : -0.08 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.021 0.001 TYR D 262 PHE 0.011 0.001 PHE D 144 TRP 0.013 0.001 TRP B 320 HIS 0.001 0.000 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (17085) covalent geometry : angle 0.52177 / 0.25 (23365) SS BOND : bond 0.00206 / 0.10 ( 5) SS BOND : angle 0.78026 / 0.47 ( 10) hydrogen bonds : bond 0.04214 / 2.70 ( 860) hydrogen bonds : angle 3.90319 / 2.68 ( 2555) link_BETA1-4 : bond 0.00430 / 0.24 ( 15) link_BETA1-4 : angle 1.24330 / 0.76 ( 45) link_NAG-ASN : bond 0.00127 / 0.07 ( 15) link_NAG-ASN : angle 1.19719 / 0.76 ( 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 163 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8441 (mt) cc_final: 0.8232 (mp) REVERT: A 199 PHE cc_start: 0.7027 (t80) cc_final: 0.6752 (t80) REVERT: A 223 TYR cc_start: 0.7183 (m-80) cc_final: 0.6778 (m-80) REVERT: A 291 MET cc_start: 0.6320 (tmm) cc_final: 0.6037 (tpp) REVERT: A 311 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6705 (pp30) REVERT: A 416 ARG cc_start: 0.6142 (mtp180) cc_final: 0.5587 (mmp-170) REVERT: A 421 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6021 (tt0) REVERT: A 456 TRP cc_start: 0.5677 (t60) cc_final: 0.4472 (t-100) REVERT: D 52 ASP cc_start: 0.6991 (t0) cc_final: 0.6376 (t0) REVERT: D 54 LYS cc_start: 0.8199 (tttm) cc_final: 0.7911 (tptm) REVERT: D 108 LYS cc_start: 0.7384 (mtmp) cc_final: 0.6989 (mtpp) REVERT: D 223 TYR cc_start: 0.6788 (m-80) cc_final: 0.6478 (m-80) REVERT: D 291 MET cc_start: 0.6810 (tpp) cc_final: 0.5249 (ttt) REVERT: D 416 ARG cc_start: 0.6015 (mtp180) cc_final: 0.5657 (mmp-170) REVERT: D 421 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6032 (tt0) REVERT: D 456 TRP cc_start: 0.5750 (t60) cc_final: 0.4546 (t-100) REVERT: B 41 ILE cc_start: 0.8572 (mt) cc_final: 0.8365 (mp) REVERT: B 52 ASP cc_start: 0.6977 (t0) cc_final: 0.6656 (t70) REVERT: B 60 THR cc_start: 0.8218 (p) cc_final: 0.8008 (t) REVERT: B 105 ASP cc_start: 0.8671 (t0) cc_final: 0.8159 (t0) REVERT: B 199 PHE cc_start: 0.6889 (t80) cc_final: 0.6530 (t80) REVERT: B 223 TYR cc_start: 0.7189 (m-80) cc_final: 0.6856 (m-80) REVERT: B 416 ARG cc_start: 0.6001 (mtp180) cc_final: 0.5475 (mmp-170) REVERT: B 421 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5924 (tt0) REVERT: B 456 TRP cc_start: 0.5824 (t60) cc_final: 0.4708 (t-100) REVERT: C 41 ILE cc_start: 0.8482 (mt) cc_final: 0.8073 (pt) REVERT: C 45 MET cc_start: 0.9167 (tpt) cc_final: 0.8881 (tpp) REVERT: C 108 LYS cc_start: 0.7307 (mtmp) cc_final: 0.7067 (mtpp) REVERT: C 418 GLU cc_start: 0.7297 (tt0) cc_final: 0.7076 (pt0) REVERT: C 421 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5613 (tt0) REVERT: C 456 TRP cc_start: 0.5860 (t60) cc_final: 0.4884 (t-100) REVERT: E 199 PHE cc_start: 0.6743 (t80) cc_final: 0.6374 (t80) REVERT: E 223 TYR cc_start: 0.7127 (m-80) cc_final: 0.6848 (m-80) REVERT: E 416 ARG cc_start: 0.5941 (mtp180) cc_final: 0.5458 (mmp-170) REVERT: E 421 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6086 (tt0) REVERT: E 456 TRP cc_start: 0.5756 (t60) cc_final: 0.4691 (t-100) outliers start: 34 outliers final: 22 residues processed: 155 average time/residue: 0.5550 time to fit residues: 97.4028 Evaluate side-chains 156 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 269 VAL 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 296 ILE Chi-restraints excluded: chain B residue 421 GLU 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 421 GLU 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 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: 0.6980 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 137 optimal weight: 0.6980 chunk 162 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN D 22 ASN C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085600 restraints weight = 73028.428| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.88 r_work: 0.2799 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17120 Z= 0.094 Angle : 0.516 10.485 23465 Z= 0.246 Chirality : 0.042 0.128 2775 Planarity : 0.004 0.038 2820 Dihedral : 5.450 47.065 2369 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.88 % Allowed : 14.75 % Favored : 83.37 % 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: 1.38 (0.20), residues: 1930 helix: 3.46 (0.18), residues: 745 sheet: -1.48 (0.23), residues: 485 loop : -0.03 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 328 TYR 0.015 0.001 TYR E 262 PHE 0.018 0.001 PHE D 144 TRP 0.014 0.001 TRP B 320 HIS 0.001 0.000 HIS E 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (17085) covalent geometry : angle 0.51163 / 0.25 (23365) SS BOND : bond 0.00166 / 0.08 ( 5) SS BOND : angle 0.70539 / 0.43 ( 10) hydrogen bonds : bond 0.03997 / 2.55 ( 860) hydrogen bonds : angle 3.84158 / 2.64 ( 2555) link_BETA1-4 : bond 0.00458 / 0.26 ( 15) link_BETA1-4 : angle 1.20932 / 0.74 ( 45) link_NAG-ASN : bond 0.00144 / 0.08 ( 15) link_NAG-ASN : angle 1.10482 / 0.69 ( 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 162 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: A 199 PHE cc_start: 0.6997 (t80) cc_final: 0.6714 (t80) REVERT: A 223 TYR cc_start: 0.7212 (m-80) cc_final: 0.6832 (m-80) REVERT: A 291 MET cc_start: 0.6274 (tmm) cc_final: 0.5982 (tpp) REVERT: A 311 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6806 (pp30) REVERT: A 421 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6016 (tt0) REVERT: A 456 TRP cc_start: 0.5684 (t60) cc_final: 0.4451 (t-100) REVERT: D 52 ASP cc_start: 0.6972 (t0) cc_final: 0.6348 (t0) REVERT: D 54 LYS cc_start: 0.8175 (tttm) cc_final: 0.7874 (tptm) REVERT: D 223 TYR cc_start: 0.6776 (m-80) cc_final: 0.6380 (m-80) REVERT: D 291 MET cc_start: 0.6498 (tpp) cc_final: 0.4890 (ttp) REVERT: D 416 ARG cc_start: 0.6003 (mtp180) cc_final: 0.5648 (mmp-170) REVERT: D 421 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5994 (tt0) REVERT: D 456 TRP cc_start: 0.5758 (t60) cc_final: 0.4601 (t-100) REVERT: B 52 ASP cc_start: 0.7033 (t0) cc_final: 0.6223 (t0) REVERT: B 60 THR cc_start: 0.8241 (p) cc_final: 0.8012 (t) REVERT: B 105 ASP cc_start: 0.8662 (t0) cc_final: 0.8161 (t0) REVERT: B 144 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: B 199 PHE cc_start: 0.6828 (t80) cc_final: 0.6511 (t80) REVERT: B 223 TYR cc_start: 0.7204 (m-80) cc_final: 0.6861 (m-80) REVERT: B 291 MET cc_start: 0.6200 (tpp) cc_final: 0.4745 (ttt) REVERT: B 421 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5945 (tt0) REVERT: B 456 TRP cc_start: 0.5465 (t60) cc_final: 0.4313 (t-100) REVERT: C 45 MET cc_start: 0.9134 (tpt) cc_final: 0.8852 (tpp) REVERT: C 108 LYS cc_start: 0.7260 (mtmp) cc_final: 0.7017 (mtpp) REVERT: C 144 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: C 421 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5654 (tt0) REVERT: C 456 TRP cc_start: 0.5831 (t60) cc_final: 0.4823 (t-100) REVERT: E 199 PHE cc_start: 0.6960 (t80) cc_final: 0.6596 (t80) REVERT: E 223 TYR cc_start: 0.7115 (m-80) cc_final: 0.6802 (m-80) REVERT: E 416 ARG cc_start: 0.5900 (mtp180) cc_final: 0.5425 (mmp-170) REVERT: E 421 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6048 (tt0) REVERT: E 456 TRP cc_start: 0.5727 (t60) cc_final: 0.4651 (t-100) outliers start: 29 outliers final: 15 residues processed: 155 average time/residue: 0.4966 time to fit residues: 87.7193 Evaluate side-chains 149 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 269 VAL 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 C residue 116 TYR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 421 GLU 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 421 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 124 optimal weight: 0.0570 chunk 51 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085333 restraints weight = 82281.049| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 5.14 r_work: 0.2784 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 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 = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17120 Z= 0.096 Angle : 0.523 9.939 23465 Z= 0.249 Chirality : 0.043 0.136 2775 Planarity : 0.004 0.038 2820 Dihedral : 5.391 46.769 2369 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.55 % Allowed : 15.41 % Favored : 83.04 % 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: 1.42 (0.20), residues: 1930 helix: 3.47 (0.18), residues: 745 sheet: -1.43 (0.23), residues: 485 loop : 0.00 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.014 0.001 TYR E 262 PHE 0.007 0.001 PHE E 254 TRP 0.013 0.001 TRP B 320 HIS 0.004 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (17085) covalent geometry : angle 0.51923 / 0.25 (23365) SS BOND : bond 0.00172 / 0.09 ( 5) SS BOND : angle 0.72214 / 0.44 ( 10) hydrogen bonds : bond 0.03956 / 2.53 ( 860) hydrogen bonds : angle 3.81645 / 2.63 ( 2555) link_BETA1-4 : bond 0.00440 / 0.25 ( 15) link_BETA1-4 : angle 1.21954 / 0.75 ( 45) link_NAG-ASN : bond 0.00139 / 0.08 ( 15) link_NAG-ASN : angle 1.11107 / 0.70 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5504.41 seconds wall clock time: 94 minutes 42.40 seconds (5682.40 seconds total)