Starting phenix.real_space_refine on Fri Sep 27 17:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/09_2024/6y1z_10673.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/09_2024/6y1z_10673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/09_2024/6y1z_10673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/09_2024/6y1z_10673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/09_2024/6y1z_10673.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/09_2024/6y1z_10673.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16610 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "D" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "B" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "C" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "E" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 384, 3169 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3222 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="O7B C 501 " pdbres="TRP C 502 " Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="O7B E 501 " pdbres="TRP E 502 " Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ATYR A 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 67 " occ=0.50 residue: pdb=" N ATRP A 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 168 " occ=0.50 residue: pdb=" N ATYR D 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 67 " occ=0.50 residue: pdb=" N ATRP D 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP D 168 " occ=0.50 residue: pdb=" N ATYR B 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 67 " occ=0.50 residue: pdb=" N ATRP B 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 168 " occ=0.50 residue: pdb=" N ATYR C 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 67 " occ=0.50 residue: pdb=" N ATRP C 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP C 168 " occ=0.50 residue: pdb=" N ATYR E 67 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 67 " occ=0.50 residue: pdb=" N ATRP E 168 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP E 168 " occ=0.50 Time building chain proxies: 17.65, per 1000 atoms: 1.06 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: 5.07 Conformation dependent library (CDL) restraints added in 4.0 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: 2.39 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: 6.52 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4239 1.33 - 1.45: 3326 1.45 - 1.57: 9450 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17085 Sorted by residual: bond pdb=" C21 O7B A 504 " pdb=" C22 O7B A 504 " ideal model delta sigma weight residual 1.554 1.521 0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" C21 O7B D 504 " pdb=" C22 O7B D 504 " ideal model delta sigma weight residual 1.554 1.521 0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C21 O7B E 501 " pdb=" C22 O7B E 501 " ideal model delta sigma weight residual 1.554 1.522 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C21 O7B C 501 " pdb=" C22 O7B C 501 " ideal model delta sigma weight residual 1.554 1.522 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C21 O7B B 504 " pdb=" C22 O7B B 504 " ideal model delta sigma weight residual 1.554 1.522 0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 17080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 22917 1.62 - 3.25: 365 3.25 - 4.87: 43 4.87 - 6.50: 25 6.50 - 8.12: 15 Bond angle restraints: 23365 Sorted by residual: angle pdb=" C06 O7B B 504 " pdb=" N05 O7B B 504 " pdb=" C15 O7B B 504 " ideal model delta sigma weight residual 116.43 124.55 -8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" C06 O7B E 501 " pdb=" N05 O7B E 501 " pdb=" C15 O7B E 501 " ideal model delta sigma weight residual 116.43 124.52 -8.09 3.00e+00 1.11e-01 7.28e+00 angle pdb=" C06 O7B C 501 " pdb=" N05 O7B C 501 " pdb=" C15 O7B C 501 " ideal model delta sigma weight residual 116.43 124.51 -8.08 3.00e+00 1.11e-01 7.26e+00 angle pdb=" C06 O7B D 504 " pdb=" N05 O7B D 504 " pdb=" C15 O7B D 504 " ideal model delta sigma weight residual 116.43 124.50 -8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" C06 O7B A 504 " pdb=" N05 O7B A 504 " pdb=" C15 O7B A 504 " ideal model delta sigma weight residual 116.43 124.48 -8.05 3.00e+00 1.11e-01 7.21e+00 ... (remaining 23360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 9997 21.52 - 43.04: 393 43.04 - 64.56: 90 64.56 - 86.09: 69 86.09 - 107.61: 26 Dihedral angle restraints: 10575 sinusoidal: 4780 harmonic: 5795 Sorted by residual: dihedral pdb=" C2 NAG M 2 " pdb=" C3 NAG M 2 " pdb=" C4 NAG M 2 " pdb=" C5 NAG M 2 " ideal model delta sinusoidal sigma weight residual 53.78 -53.83 107.61 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG K 2 " pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" C5 NAG K 2 " ideal model delta sinusoidal sigma weight residual 53.78 -53.80 107.58 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG G 2 " pdb=" C3 NAG G 2 " pdb=" C4 NAG G 2 " pdb=" C5 NAG G 2 " ideal model delta sinusoidal sigma weight residual 53.78 -53.79 107.57 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 10572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2579 0.094 - 0.187: 181 0.187 - 0.281: 10 0.281 - 0.374: 0 0.374 - 0.468: 5 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C15 O7B E 501 " pdb=" C16 O7B E 501 " pdb=" C20 O7B E 501 " pdb=" N05 O7B E 501 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C15 O7B B 504 " pdb=" C16 O7B B 504 " pdb=" C20 O7B B 504 " pdb=" N05 O7B B 504 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C15 O7B D 504 " pdb=" C16 O7B D 504 " pdb=" C20 O7B D 504 " pdb=" N05 O7B D 504 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2772 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 O7B E 501 " -0.020 2.00e-02 2.50e+03 1.51e-02 3.42e+00 pdb=" C06 O7B E 501 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B E 501 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B E 501 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B E 501 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B E 501 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 O7B D 504 " -0.020 2.00e-02 2.50e+03 1.50e-02 3.37e+00 pdb=" C06 O7B D 504 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B D 504 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B D 504 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B D 504 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B D 504 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 O7B C 501 " -0.020 2.00e-02 2.50e+03 1.48e-02 3.30e+00 pdb=" C06 O7B C 501 " 0.010 2.00e-02 2.50e+03 pdb=" C08 O7B C 501 " 0.013 2.00e-02 2.50e+03 pdb=" C15 O7B C 501 " 0.012 2.00e-02 2.50e+03 pdb=" N05 O7B C 501 " 0.007 2.00e-02 2.50e+03 pdb=" O07 O7B C 501 " -0.022 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5143 2.84 - 3.36: 14866 3.36 - 3.87: 27276 3.87 - 4.39: 30178 4.39 - 4.90: 54112 Nonbonded interactions: 131575 Sorted by model distance: nonbonded pdb=" OD1 ASP D 105 " pdb=" N VAL D 106 " model vdw 2.325 3.120 nonbonded pdb=" OD1 ASP B 105 " pdb=" N VAL B 106 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP E 105 " pdb=" N VAL E 106 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP A 105 " pdb=" N VAL A 106 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP C 105 " pdb=" N VAL C 106 " model vdw 2.326 3.120 ... (remaining 131570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 51.670 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 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:16.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17085 Z= 0.207 Angle : 0.577 8.122 23365 Z= 0.293 Chirality : 0.049 0.468 2775 Planarity : 0.003 0.034 2820 Dihedral : 15.307 107.607 6790 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.49 % Allowed : 4.70 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (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 TRP 0.005 0.001 TRP E 426 HIS 0.001 0.000 HIS B 118 PHE 0.006 0.001 PHE C 222 TYR 0.007 0.001 TYR B 64 ARG 0.002 0.000 ARG C 34 *********************** 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 fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 1.963 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: 0.6846 (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: 0.5863 (mmp-170) REVERT: E 421 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6421 (tt0) REVERT: E 456 TRP cc_start: 0.6599 (t60) cc_final: 0.5339 (t-100) outliers start: 40 outliers final: 12 residues processed: 237 average time/residue: 1.1209 time to fit residues: 299.0571 Evaluate side-chains 140 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.902 ------------------------------------------------------------------------------- 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 160 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 125 ASN D 22 ASN B 55 ASN B 101 ASN B 125 ASN C 22 ASN C 55 ASN C 111 ASN C 125 ASN E 22 ASN E 66 GLN E 125 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17085 Z= 0.240 Angle : 0.601 8.257 23365 Z= 0.292 Chirality : 0.046 0.196 2775 Planarity : 0.004 0.038 2820 Dihedral : 11.713 70.299 3004 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.48 % Allowed : 10.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1930 helix: 2.37 (0.18), residues: 745 sheet: -2.38 (0.20), residues: 490 loop : -1.40 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.003 0.000 HIS B 118 PHE 0.010 0.001 PHE A 222 TYR 0.016 0.001 TYR A 64 ARG 0.009 0.000 ARG A 328 *********************** 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 184 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8607 (t0) cc_final: 0.8110 (t0) REVERT: A 108 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7875 (mtpp) REVERT: A 144 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: A 223 TYR cc_start: 0.7876 (m-80) cc_final: 0.7644 (m-80) REVERT: A 416 ARG cc_start: 0.6519 (mtp180) cc_final: 0.6065 (mmp-170) REVERT: A 421 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: A 456 TRP cc_start: 0.6660 (t60) cc_final: 0.5336 (t-100) REVERT: D 52 ASP cc_start: 0.7773 (t0) cc_final: 0.7218 (t0) REVERT: D 54 LYS cc_start: 0.8530 (tttm) cc_final: 0.8305 (tptm) REVERT: D 144 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: D 223 TYR cc_start: 0.7435 (m-80) cc_final: 0.7191 (m-80) REVERT: D 416 ARG cc_start: 0.6424 (mtp180) cc_final: 0.6076 (mmp-170) REVERT: D 421 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: D 456 TRP cc_start: 0.6703 (t60) cc_final: 0.5465 (t-100) REVERT: B 52 ASP cc_start: 0.7676 (t0) cc_final: 0.7406 (t70) REVERT: B 105 ASP cc_start: 0.8686 (t0) cc_final: 0.8365 (t0) REVERT: B 199 PHE cc_start: 0.7480 (t80) cc_final: 0.7071 (t80) REVERT: B 223 TYR cc_start: 0.7674 (m-80) cc_final: 0.7414 (m-80) REVERT: B 291 MET cc_start: 0.7246 (ttp) cc_final: 0.6994 (tpp) REVERT: B 416 ARG cc_start: 0.6488 (mtp180) cc_final: 0.6126 (mmp-170) REVERT: B 421 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: B 456 TRP cc_start: 0.6642 (t60) cc_final: 0.5467 (t-100) REVERT: C 421 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5907 (tp30) REVERT: C 456 TRP cc_start: 0.6742 (t60) cc_final: 0.5649 (t-100) REVERT: E 223 TYR cc_start: 0.7763 (m-80) cc_final: 0.7443 (m-80) REVERT: E 416 ARG cc_start: 0.6322 (mtp180) cc_final: 0.5866 (mmp-170) REVERT: E 421 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: E 456 TRP cc_start: 0.6590 (t60) cc_final: 0.5351 (t-100) outliers start: 58 outliers final: 32 residues processed: 170 average time/residue: 1.0751 time to fit residues: 208.0618 Evaluate side-chains 147 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 453 VAL 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 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 283 ILE 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 203 ILE 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 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 317 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 22 ASN D 55 ASN C 22 ASN C 111 ASN E 22 ASN E 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17085 Z= 0.204 Angle : 0.542 7.299 23365 Z= 0.265 Chirality : 0.044 0.138 2775 Planarity : 0.004 0.040 2820 Dihedral : 7.573 65.166 3004 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.04 % Allowed : 10.77 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1930 helix: 2.81 (0.18), residues: 745 sheet: -2.05 (0.21), residues: 490 loop : -0.89 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 320 HIS 0.001 0.000 HIS E 118 PHE 0.008 0.001 PHE A 222 TYR 0.012 0.001 TYR A 64 ARG 0.008 0.000 ARG C 328 *********************** 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 fitting. rotamer outliers: 50 poor density : 122 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8645 (t0) cc_final: 0.8182 (t0) REVERT: A 108 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7895 (mtpp) REVERT: A 144 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 223 TYR cc_start: 0.7865 (m-80) cc_final: 0.7614 (m-80) REVERT: A 416 ARG cc_start: 0.6493 (mtp180) cc_final: 0.6062 (mmp-170) REVERT: A 421 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: A 456 TRP cc_start: 0.6672 (t60) cc_final: 0.5350 (t-100) REVERT: D 52 ASP cc_start: 0.7743 (t0) cc_final: 0.7195 (t0) REVERT: D 54 LYS cc_start: 0.8498 (tttm) cc_final: 0.8264 (tptm) REVERT: D 108 LYS cc_start: 0.8414 (mtmp) cc_final: 0.7984 (mtpp) REVERT: D 223 TYR cc_start: 0.7455 (m-80) cc_final: 0.7197 (m-80) REVERT: D 416 ARG cc_start: 0.6425 (mtp180) cc_final: 0.6075 (mmp-170) REVERT: D 421 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: D 456 TRP cc_start: 0.6751 (t60) cc_final: 0.5401 (t-100) REVERT: B 52 ASP cc_start: 0.7763 (t0) cc_final: 0.7456 (t70) REVERT: B 60 THR cc_start: 0.8856 (p) cc_final: 0.8509 (t) REVERT: B 105 ASP cc_start: 0.8678 (t0) cc_final: 0.8295 (t0) REVERT: B 199 PHE cc_start: 0.7477 (t80) cc_final: 0.7091 (t80) REVERT: B 223 TYR cc_start: 0.7668 (m-80) cc_final: 0.7387 (m-80) REVERT: B 291 MET cc_start: 0.7162 (ttp) cc_final: 0.6525 (ttp) REVERT: B 416 ARG cc_start: 0.6498 (mtp180) cc_final: 0.6034 (mmp-170) REVERT: B 421 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6374 (tt0) REVERT: B 456 TRP cc_start: 0.6768 (t60) cc_final: 0.5512 (t-100) REVERT: C 103 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: C 421 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5929 (tp30) REVERT: C 456 TRP cc_start: 0.6713 (t60) cc_final: 0.5549 (t-100) REVERT: E 223 TYR cc_start: 0.7728 (m-80) cc_final: 0.7424 (m-80) REVERT: E 291 MET cc_start: 0.7063 (tpp) cc_final: 0.6664 (ttp) REVERT: E 416 ARG cc_start: 0.6272 (mtp180) cc_final: 0.5802 (mmp-170) REVERT: E 421 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: E 456 TRP cc_start: 0.6639 (t60) cc_final: 0.5336 (t-100) outliers start: 50 outliers final: 27 residues processed: 164 average time/residue: 1.1547 time to fit residues: 214.2571 Evaluate side-chains 148 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 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 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 283 ILE 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 144 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 317 VAL 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 170 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN D 22 ASN D 50 ASN B 50 ASN C 22 ASN C 50 ASN E 22 ASN E 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17085 Z= 0.164 Angle : 0.507 6.969 23365 Z= 0.251 Chirality : 0.043 0.131 2775 Planarity : 0.004 0.041 2820 Dihedral : 6.519 62.538 3002 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.20 % Allowed : 10.94 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1930 helix: 3.07 (0.18), residues: 745 sheet: -1.88 (0.21), residues: 490 loop : -0.57 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 320 HIS 0.003 0.000 HIS E 309 PHE 0.007 0.001 PHE D 254 TYR 0.015 0.001 TYR D 64 ARG 0.011 0.000 ARG A 328 *********************** 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 173 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 120 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8683 (t0) cc_final: 0.8269 (t0) REVERT: A 144 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: A 223 TYR cc_start: 0.7811 (m-80) cc_final: 0.7509 (m-80) REVERT: A 291 MET cc_start: 0.6202 (tmm) cc_final: 0.5934 (tmm) REVERT: A 416 ARG cc_start: 0.6492 (mtp180) cc_final: 0.6043 (mmp-170) REVERT: A 421 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: A 456 TRP cc_start: 0.6625 (t60) cc_final: 0.5291 (t-100) REVERT: D 52 ASP cc_start: 0.7744 (t0) cc_final: 0.7187 (t0) REVERT: D 54 LYS cc_start: 0.8475 (tttm) cc_final: 0.8248 (tptm) REVERT: D 108 LYS cc_start: 0.8422 (mtmp) cc_final: 0.7948 (mtpp) REVERT: D 223 TYR cc_start: 0.7416 (m-80) cc_final: 0.7156 (m-80) REVERT: D 416 ARG cc_start: 0.6330 (mtp180) cc_final: 0.6007 (mmp-170) REVERT: D 421 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: D 456 TRP cc_start: 0.6607 (t60) cc_final: 0.5273 (t-100) REVERT: B 52 ASP cc_start: 0.7751 (t0) cc_final: 0.7429 (t70) REVERT: B 105 ASP cc_start: 0.8687 (t0) cc_final: 0.8284 (t0) REVERT: B 199 PHE cc_start: 0.7607 (t80) cc_final: 0.7294 (t80) REVERT: B 223 TYR cc_start: 0.7659 (m-80) cc_final: 0.7386 (m-80) REVERT: B 291 MET cc_start: 0.6995 (ttp) cc_final: 0.6423 (ttp) REVERT: B 416 ARG cc_start: 0.6396 (mtp180) cc_final: 0.5945 (mmp-170) REVERT: B 421 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: B 456 TRP cc_start: 0.6751 (t60) cc_final: 0.5499 (t-100) REVERT: C 45 MET cc_start: 0.9061 (tpt) cc_final: 0.8860 (tpp) REVERT: C 103 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: C 328 ARG cc_start: 0.7114 (tmm-80) cc_final: 0.6903 (tmm-80) REVERT: C 421 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5936 (tt0) REVERT: C 456 TRP cc_start: 0.6702 (t60) cc_final: 0.5540 (t-100) REVERT: E 105 ASP cc_start: 0.8660 (t0) cc_final: 0.8376 (t0) REVERT: E 223 TYR cc_start: 0.7682 (m-80) cc_final: 0.7398 (m-80) REVERT: E 416 ARG cc_start: 0.6218 (mtp180) cc_final: 0.5734 (mmp-170) REVERT: E 421 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: E 456 TRP cc_start: 0.6613 (t60) cc_final: 0.5364 (t-100) outliers start: 53 outliers final: 28 residues processed: 163 average time/residue: 1.1219 time to fit residues: 207.1358 Evaluate side-chains 152 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 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 283 ILE 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 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 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 Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.0270 chunk 104 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 0.0010 chunk 75 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 0.0070 chunk 164 optimal weight: 0.5980 chunk 46 optimal weight: 0.0000 overall best weight: 0.1266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17085 Z= 0.115 Angle : 0.488 8.701 23365 Z= 0.240 Chirality : 0.042 0.146 2775 Planarity : 0.004 0.038 2820 Dihedral : 5.963 58.749 3001 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.71 % Allowed : 12.10 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1930 helix: 3.44 (0.18), residues: 745 sheet: -1.69 (0.22), residues: 480 loop : -0.37 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 68 HIS 0.004 0.000 HIS A 309 PHE 0.027 0.001 PHE E 103 TYR 0.013 0.001 TYR D 64 ARG 0.008 0.000 ARG C 328 *********************** 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 188 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7799 (m-80) cc_final: 0.7571 (m-80) REVERT: A 421 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: A 456 TRP cc_start: 0.6536 (t60) cc_final: 0.5188 (t-100) REVERT: D 52 ASP cc_start: 0.7681 (t0) cc_final: 0.7063 (t0) REVERT: D 54 LYS cc_start: 0.8402 (tttm) cc_final: 0.8108 (tptm) REVERT: D 108 LYS cc_start: 0.8259 (mtmp) cc_final: 0.7750 (mtpp) REVERT: D 223 TYR cc_start: 0.7389 (m-80) cc_final: 0.7122 (m-80) REVERT: D 416 ARG cc_start: 0.6330 (mtp180) cc_final: 0.5996 (mmp-170) REVERT: D 421 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: D 456 TRP cc_start: 0.6521 (t60) cc_final: 0.5281 (t-100) REVERT: B 52 ASP cc_start: 0.7699 (t0) cc_final: 0.6836 (t0) REVERT: B 105 ASP cc_start: 0.8605 (t0) cc_final: 0.8199 (t0) REVERT: B 144 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: B 199 PHE cc_start: 0.7726 (t80) cc_final: 0.7438 (t80) REVERT: B 223 TYR cc_start: 0.7699 (m-80) cc_final: 0.7439 (m-80) REVERT: B 291 MET cc_start: 0.6852 (ttp) cc_final: 0.6151 (ttp) REVERT: B 421 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: B 456 TRP cc_start: 0.6559 (t60) cc_final: 0.5356 (t-100) REVERT: C 45 MET cc_start: 0.9051 (tpt) cc_final: 0.8823 (tpp) REVERT: C 108 LYS cc_start: 0.8333 (mtmp) cc_final: 0.7979 (mtpp) REVERT: C 456 TRP cc_start: 0.6689 (t60) cc_final: 0.5546 (t-100) REVERT: E 105 ASP cc_start: 0.8588 (t0) cc_final: 0.8256 (t0) REVERT: E 199 PHE cc_start: 0.7706 (t80) cc_final: 0.7495 (t80) REVERT: E 223 TYR cc_start: 0.7628 (m-80) cc_final: 0.7331 (m-80) REVERT: E 291 MET cc_start: 0.7146 (tpp) cc_final: 0.6064 (ttt) REVERT: E 416 ARG cc_start: 0.6151 (mtp180) cc_final: 0.5718 (mmp-170) REVERT: E 421 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: E 456 TRP cc_start: 0.6616 (t60) cc_final: 0.5376 (t-100) outliers start: 44 outliers final: 17 residues processed: 177 average time/residue: 0.9861 time to fit residues: 200.6581 Evaluate side-chains 149 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 421 GLU Chi-restraints excluded: chain D residue 116 TYR 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 144 PHE 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 296 ILE Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 240 VAL 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 61 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 311 GLN C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17085 Z= 0.254 Angle : 0.541 8.941 23365 Z= 0.265 Chirality : 0.044 0.140 2775 Planarity : 0.004 0.041 2820 Dihedral : 5.678 57.237 2989 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.76 % Allowed : 13.31 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1930 helix: 3.35 (0.17), residues: 745 sheet: -1.67 (0.22), residues: 490 loop : -0.20 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.003 0.001 HIS D 118 PHE 0.010 0.001 PHE E 103 TYR 0.029 0.001 TYR D 116 ARG 0.008 0.000 ARG A 328 *********************** 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 168 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 123 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7854 (m-80) cc_final: 0.7536 (m-80) REVERT: A 416 ARG cc_start: 0.6493 (mtp180) cc_final: 0.6046 (mmp-170) REVERT: A 421 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6425 (tt0) REVERT: A 456 TRP cc_start: 0.6655 (t60) cc_final: 0.5298 (t-100) REVERT: D 52 ASP cc_start: 0.7781 (t0) cc_final: 0.7172 (t0) REVERT: D 108 LYS cc_start: 0.8360 (mtmp) cc_final: 0.7917 (mtpp) REVERT: D 223 TYR cc_start: 0.7417 (m-80) cc_final: 0.7148 (m-80) REVERT: D 416 ARG cc_start: 0.6284 (mtp180) cc_final: 0.6012 (mmp-170) REVERT: D 421 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: D 456 TRP cc_start: 0.6680 (t60) cc_final: 0.5319 (t-100) REVERT: B 52 ASP cc_start: 0.7814 (t0) cc_final: 0.7499 (t70) REVERT: B 105 ASP cc_start: 0.8649 (t0) cc_final: 0.8220 (t0) REVERT: B 199 PHE cc_start: 0.7636 (t80) cc_final: 0.7323 (t80) REVERT: B 223 TYR cc_start: 0.7663 (m-80) cc_final: 0.7352 (m-80) REVERT: B 311 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: B 416 ARG cc_start: 0.6425 (mtp180) cc_final: 0.6022 (mmp-170) REVERT: B 421 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: B 456 TRP cc_start: 0.6736 (t60) cc_final: 0.5475 (t-100) REVERT: C 45 MET cc_start: 0.9086 (tpt) cc_final: 0.8870 (tpp) REVERT: C 108 LYS cc_start: 0.8302 (mtmp) cc_final: 0.7979 (mtpp) REVERT: C 416 ARG cc_start: 0.6256 (mtp180) cc_final: 0.5903 (mmp-170) REVERT: C 421 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5947 (tt0) REVERT: C 456 TRP cc_start: 0.6703 (t60) cc_final: 0.5572 (t-100) REVERT: E 223 TYR cc_start: 0.7683 (m-80) cc_final: 0.7378 (m-80) REVERT: E 416 ARG cc_start: 0.6211 (mtp180) cc_final: 0.5755 (mmp-170) REVERT: E 421 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: E 456 TRP cc_start: 0.6622 (t60) cc_final: 0.5363 (t-100) outliers start: 45 outliers final: 27 residues processed: 154 average time/residue: 1.1468 time to fit residues: 199.5510 Evaluate side-chains 151 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL 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 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 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain 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 296 ILE Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17085 Z= 0.159 Angle : 0.518 9.222 23365 Z= 0.253 Chirality : 0.043 0.152 2775 Planarity : 0.004 0.039 2820 Dihedral : 5.575 55.004 2989 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.21 % Allowed : 13.87 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1930 helix: 3.42 (0.17), residues: 745 sheet: -1.63 (0.22), residues: 490 loop : -0.12 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 68 HIS 0.002 0.000 HIS D 119 PHE 0.013 0.001 PHE A 144 TYR 0.014 0.001 TYR B 262 ARG 0.009 0.000 ARG B 328 *********************** 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 163 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7754 (t80) cc_final: 0.7549 (t80) REVERT: A 223 TYR cc_start: 0.7824 (m-80) cc_final: 0.7510 (m-80) REVERT: A 291 MET cc_start: 0.7118 (tpp) cc_final: 0.6265 (ttt) REVERT: A 416 ARG cc_start: 0.6451 (mtp180) cc_final: 0.6010 (mmp-170) REVERT: A 421 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: A 456 TRP cc_start: 0.6610 (t60) cc_final: 0.5255 (t-100) REVERT: D 52 ASP cc_start: 0.7727 (t0) cc_final: 0.7089 (t0) REVERT: D 108 LYS cc_start: 0.8337 (mtmp) cc_final: 0.7884 (mtpp) REVERT: D 223 TYR cc_start: 0.7433 (m-80) cc_final: 0.7170 (m-80) REVERT: D 416 ARG cc_start: 0.6307 (mtp180) cc_final: 0.6050 (mmp-170) REVERT: D 421 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: D 456 TRP cc_start: 0.6628 (t60) cc_final: 0.5264 (t-100) REVERT: B 52 ASP cc_start: 0.7758 (t0) cc_final: 0.7435 (t70) REVERT: B 105 ASP cc_start: 0.8651 (t0) cc_final: 0.8230 (t0) REVERT: B 199 PHE cc_start: 0.7621 (t80) cc_final: 0.7327 (t80) REVERT: B 223 TYR cc_start: 0.7641 (m-80) cc_final: 0.7336 (m-80) REVERT: B 291 MET cc_start: 0.6994 (tpp) cc_final: 0.5927 (ttt) REVERT: B 416 ARG cc_start: 0.6382 (mtp180) cc_final: 0.5940 (mmp-170) REVERT: B 421 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6352 (tt0) REVERT: B 456 TRP cc_start: 0.6680 (t60) cc_final: 0.5420 (t-100) REVERT: C 45 MET cc_start: 0.9080 (tpt) cc_final: 0.8850 (tpp) REVERT: C 108 LYS cc_start: 0.8276 (mtmp) cc_final: 0.7949 (mtpp) REVERT: C 421 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5980 (tt0) REVERT: C 456 TRP cc_start: 0.6680 (t60) cc_final: 0.5554 (t-100) REVERT: E 199 PHE cc_start: 0.7614 (t80) cc_final: 0.7379 (t80) REVERT: E 223 TYR cc_start: 0.7680 (m-80) cc_final: 0.7380 (m-80) REVERT: E 250 GLU cc_start: 0.7582 (pt0) cc_final: 0.7300 (pm20) REVERT: E 291 MET cc_start: 0.6894 (tpp) cc_final: 0.6031 (ttt) REVERT: E 416 ARG cc_start: 0.6289 (mtp180) cc_final: 0.5838 (mmp-170) REVERT: E 421 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6463 (tt0) REVERT: E 456 TRP cc_start: 0.6591 (t60) cc_final: 0.5343 (t-100) outliers start: 35 outliers final: 25 residues processed: 152 average time/residue: 1.1458 time to fit residues: 197.5768 Evaluate side-chains 150 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL 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 240 VAL 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 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 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 296 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 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 73 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 311 GLN C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17085 Z= 0.195 Angle : 0.537 9.452 23365 Z= 0.260 Chirality : 0.044 0.171 2775 Planarity : 0.004 0.040 2820 Dihedral : 5.561 52.273 2989 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.65 % Allowed : 13.81 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1930 helix: 3.34 (0.18), residues: 745 sheet: -1.76 (0.21), residues: 515 loop : -0.01 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 68 HIS 0.002 0.000 HIS D 119 PHE 0.016 0.001 PHE D 144 TYR 0.014 0.001 TYR E 64 ARG 0.007 0.000 ARG A 328 *********************** 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 166 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7795 (m-80) cc_final: 0.7459 (m-80) REVERT: A 416 ARG cc_start: 0.6496 (mtp180) cc_final: 0.6045 (mmp-170) REVERT: A 421 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: A 456 TRP cc_start: 0.6603 (t60) cc_final: 0.5233 (t-100) REVERT: D 52 ASP cc_start: 0.7757 (t0) cc_final: 0.7141 (t0) REVERT: D 223 TYR cc_start: 0.7413 (m-80) cc_final: 0.7140 (m-80) REVERT: D 416 ARG cc_start: 0.6323 (mtp180) cc_final: 0.6057 (mmp-170) REVERT: D 421 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: D 456 TRP cc_start: 0.6630 (t60) cc_final: 0.5247 (t-100) REVERT: B 52 ASP cc_start: 0.7800 (t0) cc_final: 0.7477 (t70) REVERT: B 105 ASP cc_start: 0.8690 (t0) cc_final: 0.8263 (t0) REVERT: B 199 PHE cc_start: 0.7606 (t80) cc_final: 0.7294 (t80) REVERT: B 223 TYR cc_start: 0.7638 (m-80) cc_final: 0.7326 (m-80) REVERT: B 311 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7371 (pp30) REVERT: B 416 ARG cc_start: 0.6395 (mtp180) cc_final: 0.5952 (mmp-170) REVERT: B 421 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: B 456 TRP cc_start: 0.6721 (t60) cc_final: 0.5440 (t-100) REVERT: C 45 MET cc_start: 0.9088 (tpt) cc_final: 0.8858 (tpp) REVERT: C 108 LYS cc_start: 0.8297 (mtmp) cc_final: 0.7945 (mtpp) REVERT: C 416 ARG cc_start: 0.6249 (mtp180) cc_final: 0.5898 (mmp-170) REVERT: C 421 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5989 (tt0) REVERT: C 456 TRP cc_start: 0.6694 (t60) cc_final: 0.5561 (t-100) REVERT: E 199 PHE cc_start: 0.7600 (t80) cc_final: 0.7339 (t80) REVERT: E 223 TYR cc_start: 0.7622 (m-80) cc_final: 0.7330 (m-80) REVERT: E 416 ARG cc_start: 0.6295 (mtp180) cc_final: 0.5864 (mmp-170) REVERT: E 421 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6455 (tt0) REVERT: E 456 TRP cc_start: 0.6614 (t60) cc_final: 0.5348 (t-100) outliers start: 43 outliers final: 31 residues processed: 155 average time/residue: 1.1433 time to fit residues: 200.7708 Evaluate side-chains 157 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 453 VAL 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 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 296 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 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 160 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17085 Z= 0.282 Angle : 0.576 10.034 23365 Z= 0.280 Chirality : 0.045 0.150 2775 Planarity : 0.004 0.042 2820 Dihedral : 5.631 50.427 2989 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.82 % Allowed : 13.98 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1930 helix: 3.18 (0.17), residues: 745 sheet: -1.80 (0.21), residues: 515 loop : -0.02 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.002 0.001 HIS D 119 PHE 0.031 0.002 PHE B 233 TYR 0.017 0.001 TYR E 262 ARG 0.007 0.000 ARG A 328 *********************** 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 159 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 113 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7880 (m-80) cc_final: 0.7534 (m-80) REVERT: A 250 GLU cc_start: 0.7373 (pt0) cc_final: 0.7061 (pt0) REVERT: A 416 ARG cc_start: 0.6497 (mtp180) cc_final: 0.6025 (mmp-170) REVERT: A 421 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6434 (tt0) REVERT: A 456 TRP cc_start: 0.6628 (t60) cc_final: 0.5290 (t-100) REVERT: D 52 ASP cc_start: 0.7783 (t0) cc_final: 0.7204 (t0) REVERT: D 223 TYR cc_start: 0.7480 (m-80) cc_final: 0.7244 (m-80) REVERT: D 416 ARG cc_start: 0.6273 (mtp180) cc_final: 0.6006 (mmp-170) REVERT: D 421 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6506 (tt0) REVERT: D 456 TRP cc_start: 0.6689 (t60) cc_final: 0.5283 (t-100) REVERT: B 52 ASP cc_start: 0.7788 (t0) cc_final: 0.7473 (t70) REVERT: B 105 ASP cc_start: 0.8737 (t0) cc_final: 0.8290 (t0) REVERT: B 223 TYR cc_start: 0.7657 (m-80) cc_final: 0.7322 (m-80) REVERT: B 291 MET cc_start: 0.6867 (tpp) cc_final: 0.5181 (ttt) REVERT: B 311 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7546 (pp30) REVERT: B 416 ARG cc_start: 0.6289 (mtp180) cc_final: 0.5864 (mmp-170) REVERT: B 421 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: B 456 TRP cc_start: 0.6783 (t60) cc_final: 0.5450 (t-100) REVERT: C 108 LYS cc_start: 0.8326 (mtmp) cc_final: 0.7963 (mtpp) REVERT: C 416 ARG cc_start: 0.6302 (mtp180) cc_final: 0.5911 (mmp-170) REVERT: C 421 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5869 (tp30) REVERT: C 456 TRP cc_start: 0.6622 (t60) cc_final: 0.5434 (t-100) REVERT: E 223 TYR cc_start: 0.7679 (m-80) cc_final: 0.7422 (m-80) REVERT: E 250 GLU cc_start: 0.7593 (pt0) cc_final: 0.7351 (pm20) REVERT: E 416 ARG cc_start: 0.6319 (mtp180) cc_final: 0.5897 (mmp-170) REVERT: E 421 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: E 456 TRP cc_start: 0.6690 (t60) cc_final: 0.5395 (t-100) outliers start: 46 outliers final: 32 residues processed: 148 average time/residue: 1.2401 time to fit residues: 207.3381 Evaluate side-chains 149 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 111 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 453 VAL 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 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 296 ILE 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 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 317 VAL 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 296 ILE Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 119 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 311 GLN C 22 ASN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17085 Z= 0.157 Angle : 0.531 9.109 23365 Z= 0.258 Chirality : 0.043 0.144 2775 Planarity : 0.004 0.041 2820 Dihedral : 5.488 48.026 2989 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.21 % Allowed : 14.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1930 helix: 3.35 (0.18), residues: 745 sheet: -1.72 (0.22), residues: 510 loop : 0.06 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.002 0.000 HIS B 309 PHE 0.029 0.001 PHE B 233 TYR 0.017 0.001 TYR A 262 ARG 0.007 0.000 ARG B 328 ********************** 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 159 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7779 (m-80) cc_final: 0.7446 (m-80) REVERT: A 416 ARG cc_start: 0.6499 (mtp180) cc_final: 0.6041 (mmp-170) REVERT: A 421 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: A 456 TRP cc_start: 0.6700 (t60) cc_final: 0.5366 (t-100) REVERT: D 52 ASP cc_start: 0.7737 (t0) cc_final: 0.7113 (t0) REVERT: D 108 LYS cc_start: 0.8329 (mtmp) cc_final: 0.7831 (mtpp) REVERT: D 223 TYR cc_start: 0.7423 (m-80) cc_final: 0.7204 (m-80) REVERT: D 416 ARG cc_start: 0.6319 (mtp180) cc_final: 0.6052 (mmp-170) REVERT: D 421 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6488 (tt0) REVERT: D 456 TRP cc_start: 0.6655 (t60) cc_final: 0.5276 (t-100) REVERT: B 52 ASP cc_start: 0.7767 (t0) cc_final: 0.7448 (t70) REVERT: B 105 ASP cc_start: 0.8667 (t0) cc_final: 0.8244 (t0) REVERT: B 199 PHE cc_start: 0.7669 (t80) cc_final: 0.7325 (t80) REVERT: B 223 TYR cc_start: 0.7612 (m-80) cc_final: 0.7298 (m-80) REVERT: B 291 MET cc_start: 0.6819 (tpp) cc_final: 0.5209 (ttt) REVERT: B 311 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7398 (pp30) REVERT: B 416 ARG cc_start: 0.6381 (mtp180) cc_final: 0.5950 (mmp-170) REVERT: B 421 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: B 456 TRP cc_start: 0.6740 (t60) cc_final: 0.5436 (t-100) REVERT: C 108 LYS cc_start: 0.8284 (mtmp) cc_final: 0.7912 (mtpp) REVERT: C 416 ARG cc_start: 0.6248 (mtp180) cc_final: 0.5894 (mmp-170) REVERT: C 421 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5980 (tt0) REVERT: C 456 TRP cc_start: 0.6612 (t60) cc_final: 0.5436 (t-100) REVERT: E 199 PHE cc_start: 0.7576 (t80) cc_final: 0.7237 (t80) REVERT: E 223 TYR cc_start: 0.7682 (m-80) cc_final: 0.7437 (m-80) REVERT: E 416 ARG cc_start: 0.6297 (mtp180) cc_final: 0.5865 (mmp-170) REVERT: E 421 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: E 456 TRP cc_start: 0.6584 (t60) cc_final: 0.5321 (t-100) outliers start: 35 outliers final: 25 residues processed: 150 average time/residue: 1.2638 time to fit residues: 212.6271 Evaluate side-chains 150 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 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 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 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 317 VAL 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 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 46 optimal weight: 0.2980 chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083763 restraints weight = 77344.040| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 5.09 r_work: 0.2793 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17085 Z= 0.174 Angle : 0.541 9.215 23365 Z= 0.261 Chirality : 0.044 0.198 2775 Planarity : 0.004 0.042 2820 Dihedral : 5.455 47.748 2989 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.10 % Allowed : 14.75 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1930 helix: 3.35 (0.18), residues: 745 sheet: -1.72 (0.21), residues: 515 loop : 0.09 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 68 HIS 0.001 0.000 HIS D 119 PHE 0.028 0.001 PHE B 233 TYR 0.016 0.001 TYR A 262 ARG 0.008 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4765.15 seconds wall clock time: 84 minutes 39.95 seconds (5079.95 seconds total)