Starting phenix.real_space_refine on Fri Feb 16 21:36:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1z_10673/02_2024/6y1z_10673_updated.pdb" } 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 Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E ARG 439": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16610 Number of models: 1 Model: "" Number of chains: 20 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="HIS A 502 " pdbres="NAG A 503 " Not linked: pdbres="NAG A 503 " pdbres="O7B A 504 " 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="HIS D 502 " pdbres="NAG D 503 " Not linked: pdbres="NAG D 503 " pdbres="O7B D 504 " 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="HIS B 502 " pdbres="NAG B 503 " Not linked: pdbres="NAG B 503 " pdbres="O7B B 504 " 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="O7B C 501 " pdbres="TRP C 502 " Not linked: pdbres="HIS C 503 " pdbres="NAG C 504 " 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 1, 'O7B': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="O7B E 501 " pdbres="TRP E 502 " Not linked: pdbres="HIS E 503 " pdbres="NAG E 504 " 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: 16.60, per 1000 atoms: 1.00 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 - 3.50 Amino acid : False - 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: 6.80 Conformation dependent library (CDL) restraints added in 6.2 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 41.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 220 through 243 removed outlier: 3.646A pdb=" N ALA A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL A 225 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.742A pdb=" N PHE A 242 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 Processing helix chain 'A' and resid 283 through 308 Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 398 through 457 Processing helix chain 'D' and resid 13 through 20 Processing helix chain 'D' and resid 77 through 80 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.646A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL D 225 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU D 228 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU D 229 " --> pdb=" O SER D 226 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.742A pdb=" N PHE D 242 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 269 Processing helix chain 'D' and resid 283 through 308 Processing helix chain 'D' and resid 319 through 328 Processing helix chain 'D' and resid 398 through 457 Processing helix chain 'B' and resid 13 through 20 Processing helix chain 'B' and resid 77 through 80 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 220 through 243 removed outlier: 3.646A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU B 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU B 229 " --> pdb=" O SER B 226 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 3.741A pdb=" N PHE B 242 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 269 Processing helix chain 'B' and resid 283 through 308 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 398 through 457 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 220 through 243 removed outlier: 3.647A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL C 225 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 229 " --> pdb=" O SER C 226 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.741A pdb=" N PHE C 242 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 269 Processing helix chain 'C' and resid 283 through 308 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 398 through 457 Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 77 through 80 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 220 through 243 removed outlier: 3.647A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL E 225 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 228 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU E 229 " --> pdb=" O SER E 226 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 3.742A pdb=" N PHE E 242 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 269 Processing helix chain 'E' and resid 283 through 308 Processing helix chain 'E' and resid 319 through 328 Processing helix chain 'E' and resid 398 through 457 Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.116A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, 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: 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= E, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.116A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= H, 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: 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= I, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.116A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= L, 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: 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= M, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.117A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= P, 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: 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= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.115A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, 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: 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) 830 hydrogen bonds defined for protein. 2255 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: 5.21 Time building geometry restraints manager: 7.25 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=" C03 O7B C 501 " pdb=" C04 O7B C 501 " ideal model delta sigma weight residual 0.971 1.526 -0.555 2.00e-02 2.50e+03 7.69e+02 bond pdb=" C03 O7B D 504 " pdb=" C04 O7B D 504 " ideal model delta sigma weight residual 0.971 1.526 -0.555 2.00e-02 2.50e+03 7.69e+02 bond pdb=" C03 O7B E 501 " pdb=" C04 O7B E 501 " ideal model delta sigma weight residual 0.971 1.525 -0.554 2.00e-02 2.50e+03 7.68e+02 bond pdb=" C03 O7B B 504 " pdb=" C04 O7B B 504 " ideal model delta sigma weight residual 0.971 1.525 -0.554 2.00e-02 2.50e+03 7.67e+02 bond pdb=" C03 O7B A 504 " pdb=" C04 O7B A 504 " ideal model delta sigma weight residual 0.971 1.525 -0.554 2.00e-02 2.50e+03 7.67e+02 ... (remaining 17080 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.27: 704 107.27 - 113.96: 10006 113.96 - 120.66: 6753 120.66 - 127.35: 5644 127.35 - 134.05: 258 Bond angle restraints: 23365 Sorted by residual: angle pdb=" C04 O7B C 501 " pdb=" C03 O7B C 501 " pdb=" C09 O7B C 501 " ideal model delta sigma weight residual 118.02 107.24 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C04 O7B E 501 " pdb=" C03 O7B E 501 " pdb=" C09 O7B E 501 " ideal model delta sigma weight residual 118.02 107.27 10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C04 O7B B 504 " pdb=" C03 O7B B 504 " pdb=" C09 O7B B 504 " ideal model delta sigma weight residual 118.02 107.28 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C04 O7B D 504 " pdb=" C03 O7B D 504 " pdb=" C09 O7B D 504 " ideal model delta sigma weight residual 118.02 107.30 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C04 O7B A 504 " pdb=" C03 O7B A 504 " pdb=" C09 O7B A 504 " ideal model delta sigma weight residual 118.02 107.31 10.71 3.00e+00 1.11e-01 1.27e+01 ... (remaining 23360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 9900 23.27 - 46.54: 380 46.54 - 69.81: 85 69.81 - 93.08: 55 93.08 - 116.35: 45 Dihedral angle restraints: 10465 sinusoidal: 4670 harmonic: 5795 Sorted by residual: dihedral pdb=" C16 O7B D 504 " pdb=" C15 O7B D 504 " pdb=" C20 O7B D 504 " pdb=" C21 O7B D 504 " ideal model delta sinusoidal sigma weight residual -51.34 65.01 -116.35 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C16 O7B A 504 " pdb=" C15 O7B A 504 " pdb=" C20 O7B A 504 " pdb=" C21 O7B A 504 " ideal model delta sinusoidal sigma weight residual -51.34 64.99 -116.33 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C16 O7B C 501 " pdb=" C15 O7B C 501 " pdb=" C20 O7B C 501 " pdb=" C21 O7B C 501 " ideal model delta sinusoidal sigma weight residual -51.34 64.98 -116.32 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 10462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.096: 2765 1.096 - 2.193: 0 2.193 - 3.289: 0 3.289 - 4.385: 5 4.385 - 5.481: 5 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C20 O7B C 501 " pdb=" C15 O7B C 501 " pdb=" C19 O7B C 501 " pdb=" C21 O7B C 501 " both_signs ideal model delta sigma weight residual False 2.71 -2.77 5.48 2.00e-01 2.50e+01 7.51e+02 chirality pdb=" C20 O7B D 504 " pdb=" C15 O7B D 504 " pdb=" C19 O7B D 504 " pdb=" C21 O7B D 504 " both_signs ideal model delta sigma weight residual False 2.71 -2.77 5.48 2.00e-01 2.50e+01 7.51e+02 chirality pdb=" C20 O7B B 504 " pdb=" C15 O7B B 504 " pdb=" C19 O7B B 504 " pdb=" C21 O7B B 504 " both_signs ideal model delta sigma weight residual False 2.71 -2.77 5.48 2.00e-01 2.50e+01 7.51e+02 ... (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: 5148 2.84 - 3.36: 14896 3.36 - 3.87: 27346 3.87 - 4.39: 30193 4.39 - 4.90: 54117 Nonbonded interactions: 131700 Sorted by model distance: nonbonded pdb=" OD1 ASP D 105 " pdb=" N VAL D 106 " model vdw 2.325 2.520 nonbonded pdb=" OD1 ASP B 105 " pdb=" N VAL B 106 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP E 105 " pdb=" N VAL E 106 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP A 105 " pdb=" N VAL A 106 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP C 105 " pdb=" N VAL C 106 " model vdw 2.326 2.520 ... (remaining 131695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'B' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'C' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'D' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) selection = (chain 'E' and (resid 8 through 66 or resid 68 through 167 or resid 169 through \ 458)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 3.830 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 57.630 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.150 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.000 ------------------------------------------------------------------------------- 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 : 0.014 0.555 17085 Z= 0.952 Angle : 0.688 10.776 23365 Z= 0.318 Chirality : 0.282 5.481 2775 Planarity : 0.003 0.034 2820 Dihedral : 17.066 116.349 6680 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 : 1.940 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: 1.1628 time to fit residues: 309.4728 Evaluate side-chains 140 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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: 0.0570 chunk 144 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- 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 ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 125 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 111 ASN C 125 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 66 GLN E 125 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17085 Z= 0.194 Angle : 0.872 21.030 23365 Z= 0.353 Chirality : 0.133 2.947 2775 Planarity : 0.004 0.037 2820 Dihedral : 15.778 140.747 2894 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.20 % Allowed : 10.11 % Favored : 86.69 % 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: -0.38 (0.19), residues: 1930 helix: 2.19 (0.19), residues: 745 sheet: -2.21 (0.20), residues: 480 loop : -1.42 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.001 0.000 HIS D 323 PHE 0.008 0.001 PHE E 222 TYR 0.016 0.001 TYR D 223 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 171 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 118 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7604 (t0) cc_final: 0.7044 (t0) REVERT: A 54 LYS cc_start: 0.8447 (tttm) cc_final: 0.8243 (tttm) REVERT: A 105 ASP cc_start: 0.8465 (t0) cc_final: 0.8011 (t0) REVERT: A 108 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7868 (mtpt) REVERT: A 144 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: A 416 ARG cc_start: 0.6525 (mtp180) cc_final: 0.6016 (mmp-170) REVERT: A 421 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: A 456 TRP cc_start: 0.6580 (t60) cc_final: 0.5219 (t-100) REVERT: D 52 ASP cc_start: 0.7671 (t0) cc_final: 0.7143 (t0) REVERT: D 54 LYS cc_start: 0.8511 (tttm) cc_final: 0.8303 (tptm) REVERT: D 416 ARG cc_start: 0.6374 (mtp180) cc_final: 0.5982 (mmp-170) REVERT: D 421 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6400 (tt0) REVERT: D 456 TRP cc_start: 0.6633 (t60) cc_final: 0.5451 (t-100) REVERT: B 52 ASP cc_start: 0.7695 (t0) cc_final: 0.7415 (t70) REVERT: B 60 THR cc_start: 0.8921 (p) cc_final: 0.8608 (t) REVERT: B 105 ASP cc_start: 0.8480 (t0) cc_final: 0.8152 (t0) REVERT: B 291 MET cc_start: 0.7213 (ttp) cc_final: 0.6500 (ttp) REVERT: B 416 ARG cc_start: 0.6477 (mtp180) cc_final: 0.6095 (mmp-170) REVERT: B 421 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6385 (tt0) REVERT: B 456 TRP cc_start: 0.6560 (t60) cc_final: 0.5387 (t-100) REVERT: C 41 ILE cc_start: 0.8503 (mt) cc_final: 0.8288 (pt) REVERT: C 421 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5886 (tp30) REVERT: C 456 TRP cc_start: 0.6701 (t60) cc_final: 0.5582 (t-100) REVERT: E 45 MET cc_start: 0.8967 (mmm) cc_final: 0.8194 (tpt) REVERT: E 199 PHE cc_start: 0.7731 (t80) cc_final: 0.7481 (t80) REVERT: E 416 ARG cc_start: 0.6202 (mtp180) cc_final: 0.5724 (mmp-170) REVERT: E 421 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6440 (tt0) REVERT: E 456 TRP cc_start: 0.6544 (t60) cc_final: 0.5311 (t-100) outliers start: 53 outliers final: 23 residues processed: 160 average time/residue: 1.1575 time to fit residues: 209.1244 Evaluate side-chains 136 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 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 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 55 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 55 ASN C 111 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 55 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17085 Z= 0.199 Angle : 0.859 21.158 23365 Z= 0.343 Chirality : 0.126 2.790 2775 Planarity : 0.004 0.037 2820 Dihedral : 12.736 142.916 2892 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.04 % Allowed : 10.83 % Favored : 86.13 % 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: 0.23 (0.19), residues: 1930 helix: 2.54 (0.19), residues: 740 sheet: -1.81 (0.20), residues: 480 loop : -0.94 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 320 HIS 0.002 0.000 HIS B 118 PHE 0.014 0.001 PHE B 199 TYR 0.009 0.001 TYR A 64 ARG 0.009 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 174 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7578 (t0) cc_final: 0.6979 (t0) REVERT: A 54 LYS cc_start: 0.8476 (tttm) cc_final: 0.8239 (tttm) REVERT: A 105 ASP cc_start: 0.8484 (t0) cc_final: 0.8016 (t0) REVERT: A 108 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7891 (mtpp) REVERT: A 144 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: A 416 ARG cc_start: 0.6497 (mtp180) cc_final: 0.6035 (mmp-170) REVERT: A 421 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6439 (tt0) REVERT: A 456 TRP cc_start: 0.6606 (t60) cc_final: 0.5308 (t-100) REVERT: D 52 ASP cc_start: 0.7680 (t0) cc_final: 0.7112 (t0) REVERT: D 54 LYS cc_start: 0.8516 (tttm) cc_final: 0.8279 (tptm) REVERT: D 108 LYS cc_start: 0.8342 (mtmp) cc_final: 0.7901 (mtpp) REVERT: D 416 ARG cc_start: 0.6395 (mtp180) cc_final: 0.6010 (mmp-170) REVERT: D 421 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6425 (tt0) REVERT: D 456 TRP cc_start: 0.6610 (t60) cc_final: 0.5443 (t-100) REVERT: B 52 ASP cc_start: 0.7652 (t0) cc_final: 0.7357 (t70) REVERT: B 105 ASP cc_start: 0.8477 (t0) cc_final: 0.8146 (t0) REVERT: B 291 MET cc_start: 0.7079 (ttp) cc_final: 0.6412 (ttp) REVERT: B 416 ARG cc_start: 0.6502 (mtp180) cc_final: 0.6030 (mmp-170) REVERT: B 421 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6377 (tt0) REVERT: B 456 TRP cc_start: 0.6576 (t60) cc_final: 0.5420 (t-100) REVERT: C 421 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5991 (tp30) REVERT: C 456 TRP cc_start: 0.6697 (t60) cc_final: 0.5582 (t-100) REVERT: E 199 PHE cc_start: 0.7763 (t80) cc_final: 0.7519 (t80) REVERT: E 291 MET cc_start: 0.7035 (tpp) cc_final: 0.6586 (ttp) REVERT: E 416 ARG cc_start: 0.6197 (mtp180) cc_final: 0.5719 (mmp-170) REVERT: E 421 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6438 (tt0) REVERT: E 456 TRP cc_start: 0.6529 (t60) cc_final: 0.5284 (t-100) outliers start: 50 outliers final: 27 residues processed: 167 average time/residue: 1.0901 time to fit residues: 207.7168 Evaluate side-chains 141 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 242 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 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 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 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 0.0670 chunk 173 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 50 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 50 ASN C 111 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 50 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17085 Z= 0.171 Angle : 0.839 21.165 23365 Z= 0.333 Chirality : 0.126 2.803 2775 Planarity : 0.004 0.049 2820 Dihedral : 12.122 143.124 2891 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.09 % Allowed : 11.55 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.20), residues: 1930 helix: 2.82 (0.18), residues: 740 sheet: -1.56 (0.21), residues: 475 loop : -0.58 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 320 HIS 0.002 0.000 HIS E 309 PHE 0.011 0.001 PHE D 144 TYR 0.008 0.001 TYR D 64 ARG 0.010 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 172 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 121 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7547 (t0) cc_final: 0.6595 (t0) REVERT: A 54 LYS cc_start: 0.8564 (tttm) cc_final: 0.8294 (tttm) REVERT: A 105 ASP cc_start: 0.8493 (t0) cc_final: 0.7993 (t0) REVERT: A 108 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7882 (mtpp) REVERT: A 144 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: A 291 MET cc_start: 0.6238 (tmm) cc_final: 0.5973 (tmm) REVERT: A 416 ARG cc_start: 0.6441 (mtp180) cc_final: 0.5989 (mmp-170) REVERT: A 421 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 456 TRP cc_start: 0.6625 (t60) cc_final: 0.5330 (t-100) REVERT: D 52 ASP cc_start: 0.7613 (t0) cc_final: 0.6937 (t0) REVERT: D 54 LYS cc_start: 0.8535 (tttm) cc_final: 0.8335 (tptm) REVERT: D 108 LYS cc_start: 0.8354 (mtmp) cc_final: 0.7908 (mtpp) REVERT: D 416 ARG cc_start: 0.6324 (mtp180) cc_final: 0.5976 (mmp-170) REVERT: D 421 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: D 456 TRP cc_start: 0.6411 (t60) cc_final: 0.5224 (t-100) REVERT: B 52 ASP cc_start: 0.7604 (t0) cc_final: 0.7324 (t70) REVERT: B 105 ASP cc_start: 0.8502 (t0) cc_final: 0.8146 (t0) REVERT: B 291 MET cc_start: 0.6876 (ttp) cc_final: 0.6142 (ttp) REVERT: B 416 ARG cc_start: 0.6453 (mtp180) cc_final: 0.6019 (mmp-170) REVERT: B 421 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6317 (tt0) REVERT: B 456 TRP cc_start: 0.6474 (t60) cc_final: 0.5308 (t-100) REVERT: C 52 ASP cc_start: 0.7638 (t0) cc_final: 0.6675 (t0) REVERT: C 421 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5934 (tt0) REVERT: C 456 TRP cc_start: 0.6679 (t60) cc_final: 0.5558 (t-100) REVERT: E 45 MET cc_start: 0.8798 (mmm) cc_final: 0.8026 (tpt) REVERT: E 416 ARG cc_start: 0.6165 (mtp180) cc_final: 0.5706 (mmp-170) REVERT: E 421 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: E 456 TRP cc_start: 0.6513 (t60) cc_final: 0.5314 (t-100) outliers start: 51 outliers final: 31 residues processed: 162 average time/residue: 1.0913 time to fit residues: 201.3660 Evaluate side-chains 146 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 242 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 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 242 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 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 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 E residue 41 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 242 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN D 22 ASN D 314 GLN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 22 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17085 Z= 0.174 Angle : 0.843 21.142 23365 Z= 0.333 Chirality : 0.126 2.801 2775 Planarity : 0.004 0.036 2820 Dihedral : 11.965 142.967 2891 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.82 % Allowed : 12.82 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.20), residues: 1930 helix: 2.97 (0.18), residues: 740 sheet: -1.40 (0.22), residues: 470 loop : -0.42 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 320 HIS 0.002 0.000 HIS A 502 PHE 0.020 0.001 PHE E 199 TYR 0.009 0.001 TYR C 64 ARG 0.010 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 165 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 119 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7551 (t0) cc_final: 0.6595 (t0) REVERT: A 54 LYS cc_start: 0.8562 (tttm) cc_final: 0.8293 (tttm) REVERT: A 105 ASP cc_start: 0.8503 (t0) cc_final: 0.7996 (t0) REVERT: A 108 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7902 (mtpp) REVERT: A 144 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: A 291 MET cc_start: 0.6049 (tmm) cc_final: 0.5780 (tmm) REVERT: A 416 ARG cc_start: 0.6447 (mtp180) cc_final: 0.5980 (mmp-170) REVERT: A 421 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 456 TRP cc_start: 0.6626 (t60) cc_final: 0.5338 (t-100) REVERT: D 52 ASP cc_start: 0.7594 (t0) cc_final: 0.6856 (t0) REVERT: D 54 LYS cc_start: 0.8541 (tttm) cc_final: 0.8338 (tptm) REVERT: D 108 LYS cc_start: 0.8345 (mtmp) cc_final: 0.7892 (mtpp) REVERT: D 416 ARG cc_start: 0.6363 (mtp180) cc_final: 0.6025 (mmp-170) REVERT: D 421 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: D 456 TRP cc_start: 0.6502 (t60) cc_final: 0.5189 (t-100) REVERT: B 17 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: B 52 ASP cc_start: 0.7624 (t0) cc_final: 0.7293 (t70) REVERT: B 105 ASP cc_start: 0.8516 (t0) cc_final: 0.8155 (t0) REVERT: B 416 ARG cc_start: 0.6429 (mtp180) cc_final: 0.6005 (mmp-170) REVERT: B 421 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6327 (tt0) REVERT: B 456 TRP cc_start: 0.6529 (t60) cc_final: 0.5332 (t-100) REVERT: C 52 ASP cc_start: 0.7638 (t0) cc_final: 0.6676 (t0) REVERT: C 108 LYS cc_start: 0.8365 (mtmp) cc_final: 0.8000 (mtpp) REVERT: C 418 GLU cc_start: 0.7413 (tt0) cc_final: 0.7212 (pt0) REVERT: C 421 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5966 (tt0) REVERT: C 456 TRP cc_start: 0.6675 (t60) cc_final: 0.5553 (t-100) REVERT: E 45 MET cc_start: 0.8738 (mmm) cc_final: 0.7938 (tpt) REVERT: E 291 MET cc_start: 0.7279 (tpp) cc_final: 0.6373 (ttp) REVERT: E 416 ARG cc_start: 0.6165 (mtp180) cc_final: 0.5723 (mmp-170) REVERT: E 421 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6456 (tt0) REVERT: E 456 TRP cc_start: 0.6577 (t60) cc_final: 0.5375 (t-100) outliers start: 46 outliers final: 32 residues processed: 157 average time/residue: 1.1518 time to fit residues: 206.0994 Evaluate side-chains 151 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU 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 242 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 242 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 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 242 PHE 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 41 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 242 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 152 optimal weight: 0.0000 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 22 ASN D 314 GLN B 314 GLN C 22 ASN C 314 GLN E 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17085 Z= 0.199 Angle : 0.847 21.260 23365 Z= 0.336 Chirality : 0.126 2.797 2775 Planarity : 0.004 0.039 2820 Dihedral : 11.871 143.146 2889 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.09 % Allowed : 13.04 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.20), residues: 1930 helix: 3.00 (0.18), residues: 740 sheet: -1.34 (0.22), residues: 475 loop : -0.35 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 320 HIS 0.002 0.000 HIS C 309 PHE 0.016 0.001 PHE E 199 TYR 0.011 0.001 TYR B 262 ARG 0.011 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: 51 poor density : 117 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8479 (t0) cc_final: 0.7975 (t0) REVERT: A 108 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7956 (mtpp) REVERT: A 144 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: A 416 ARG cc_start: 0.6425 (mtp180) cc_final: 0.5996 (mmp-170) REVERT: A 421 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: A 456 TRP cc_start: 0.6682 (t60) cc_final: 0.5339 (t-100) REVERT: D 52 ASP cc_start: 0.7580 (t0) cc_final: 0.6862 (t0) REVERT: D 54 LYS cc_start: 0.8548 (tttm) cc_final: 0.8346 (tptm) REVERT: D 108 LYS cc_start: 0.8287 (mtmp) cc_final: 0.7811 (mtpp) REVERT: D 416 ARG cc_start: 0.6306 (mtp180) cc_final: 0.6004 (mmp-170) REVERT: D 421 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6422 (tt0) REVERT: D 456 TRP cc_start: 0.6638 (t60) cc_final: 0.5283 (t-100) REVERT: B 17 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: B 52 ASP cc_start: 0.7558 (t0) cc_final: 0.7247 (t70) REVERT: B 105 ASP cc_start: 0.8577 (t0) cc_final: 0.8169 (t0) REVERT: B 416 ARG cc_start: 0.6439 (mtp180) cc_final: 0.6003 (mmp-170) REVERT: B 421 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: B 456 TRP cc_start: 0.6660 (t60) cc_final: 0.5371 (t-100) REVERT: C 108 LYS cc_start: 0.8420 (mtmp) cc_final: 0.8010 (mtpp) REVERT: C 416 ARG cc_start: 0.6265 (mtp180) cc_final: 0.5908 (mmp-170) REVERT: C 421 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5980 (tt0) REVERT: C 456 TRP cc_start: 0.6712 (t60) cc_final: 0.5604 (t-100) REVERT: E 45 MET cc_start: 0.8721 (mmm) cc_final: 0.8062 (tpt) REVERT: E 52 ASP cc_start: 0.7625 (t0) cc_final: 0.6728 (t0) REVERT: E 416 ARG cc_start: 0.6177 (mtp180) cc_final: 0.5734 (mmp-170) REVERT: E 421 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: E 456 TRP cc_start: 0.6560 (t60) cc_final: 0.5322 (t-100) outliers start: 51 outliers final: 37 residues processed: 158 average time/residue: 1.1465 time to fit residues: 205.1349 Evaluate side-chains 161 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 242 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 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 PHE 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 C residue 450 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 113 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 314 GLN C 22 ASN C 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17085 Z= 0.212 Angle : 0.855 21.307 23365 Z= 0.339 Chirality : 0.126 2.795 2775 Planarity : 0.004 0.035 2820 Dihedral : 11.823 143.136 2889 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.15 % Allowed : 13.26 % Favored : 83.59 % 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: 1.01 (0.20), residues: 1930 helix: 2.99 (0.18), residues: 740 sheet: -1.36 (0.22), residues: 480 loop : -0.28 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 156 HIS 0.002 0.000 HIS A 502 PHE 0.016 0.001 PHE E 199 TYR 0.013 0.001 TYR B 262 ARG 0.009 0.000 ARG C 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 168 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 116 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8484 (t0) cc_final: 0.7969 (t0) REVERT: A 108 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7971 (mtpp) REVERT: A 144 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: A 250 GLU cc_start: 0.7692 (pt0) cc_final: 0.7338 (pt0) REVERT: A 416 ARG cc_start: 0.6450 (mtp180) cc_final: 0.6012 (mmp-170) REVERT: A 421 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: A 456 TRP cc_start: 0.6645 (t60) cc_final: 0.5305 (t-100) REVERT: D 52 ASP cc_start: 0.7575 (t0) cc_final: 0.6874 (t0) REVERT: D 108 LYS cc_start: 0.8296 (mtmp) cc_final: 0.7823 (mtpp) REVERT: D 416 ARG cc_start: 0.6310 (mtp180) cc_final: 0.6045 (mmp-170) REVERT: D 421 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6488 (tt0) REVERT: D 456 TRP cc_start: 0.6634 (t60) cc_final: 0.5303 (t-100) REVERT: B 52 ASP cc_start: 0.7536 (t0) cc_final: 0.7228 (t70) REVERT: B 105 ASP cc_start: 0.8611 (t0) cc_final: 0.8213 (t0) REVERT: B 416 ARG cc_start: 0.6401 (mtp180) cc_final: 0.6029 (mmp-170) REVERT: B 421 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: B 456 TRP cc_start: 0.6706 (t60) cc_final: 0.5396 (t-100) REVERT: C 108 LYS cc_start: 0.8319 (mtmp) cc_final: 0.7957 (mtpp) REVERT: C 416 ARG cc_start: 0.6236 (mtp180) cc_final: 0.5896 (mmp-170) REVERT: C 421 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5984 (tt0) REVERT: C 456 TRP cc_start: 0.6788 (t60) cc_final: 0.5668 (t-100) REVERT: E 45 MET cc_start: 0.8706 (mmm) cc_final: 0.8059 (tpt) REVERT: E 52 ASP cc_start: 0.7640 (t0) cc_final: 0.6667 (t0) REVERT: E 291 MET cc_start: 0.7048 (tpp) cc_final: 0.5934 (ttt) REVERT: E 416 ARG cc_start: 0.6285 (mtp180) cc_final: 0.5838 (mmp-170) REVERT: E 421 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: E 456 TRP cc_start: 0.6555 (t60) cc_final: 0.5346 (t-100) outliers start: 52 outliers final: 41 residues processed: 154 average time/residue: 1.2150 time to fit residues: 210.5750 Evaluate side-chains 159 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 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 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.0670 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN B 314 GLN C 22 ASN E 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17085 Z= 0.169 Angle : 0.843 21.257 23365 Z= 0.333 Chirality : 0.126 2.798 2775 Planarity : 0.004 0.037 2820 Dihedral : 11.717 142.817 2889 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.93 % Allowed : 13.48 % Favored : 83.59 % 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: 1.17 (0.20), residues: 1930 helix: 3.09 (0.18), residues: 740 sheet: -1.25 (0.22), residues: 475 loop : -0.17 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.001 0.000 HIS D 119 PHE 0.015 0.001 PHE E 199 TYR 0.014 0.001 TYR B 262 ARG 0.011 0.000 ARG B 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 173 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: A 105 ASP cc_start: 0.8473 (t0) cc_final: 0.7862 (t0) REVERT: A 108 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7944 (mtpp) REVERT: A 144 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: A 291 MET cc_start: 0.7128 (tpp) cc_final: 0.6104 (ttt) REVERT: A 416 ARG cc_start: 0.6435 (mtp180) cc_final: 0.5978 (mmp-170) REVERT: A 421 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: A 456 TRP cc_start: 0.6626 (t60) cc_final: 0.5323 (t-100) REVERT: D 52 ASP cc_start: 0.7561 (t0) cc_final: 0.6851 (t0) REVERT: D 103 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: D 108 LYS cc_start: 0.8262 (mtmp) cc_final: 0.7762 (mtpp) REVERT: D 416 ARG cc_start: 0.6292 (mtp180) cc_final: 0.6014 (mmp-170) REVERT: D 421 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: D 456 TRP cc_start: 0.6595 (t60) cc_final: 0.5264 (t-100) REVERT: B 52 ASP cc_start: 0.7578 (t0) cc_final: 0.7277 (t70) REVERT: B 105 ASP cc_start: 0.8565 (t0) cc_final: 0.8154 (t0) REVERT: B 416 ARG cc_start: 0.6428 (mtp180) cc_final: 0.6004 (mmp-170) REVERT: B 421 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6374 (tt0) REVERT: B 456 TRP cc_start: 0.6589 (t60) cc_final: 0.5299 (t-100) REVERT: C 52 ASP cc_start: 0.7659 (t0) cc_final: 0.7415 (t70) REVERT: C 108 LYS cc_start: 0.8293 (mtmp) cc_final: 0.7917 (mtpp) REVERT: C 199 PHE cc_start: 0.7731 (t80) cc_final: 0.7528 (t80) REVERT: C 416 ARG cc_start: 0.6210 (mtp180) cc_final: 0.5883 (mmp-170) REVERT: C 421 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5992 (tt0) REVERT: C 456 TRP cc_start: 0.6760 (t60) cc_final: 0.5646 (t-100) REVERT: E 45 MET cc_start: 0.8675 (mmm) cc_final: 0.7913 (tpt) REVERT: E 52 ASP cc_start: 0.7667 (t0) cc_final: 0.6713 (t0) REVERT: E 283 ILE cc_start: 0.6029 (OUTLIER) cc_final: 0.5799 (pp) REVERT: E 416 ARG cc_start: 0.6256 (mtp180) cc_final: 0.5819 (mmp-170) REVERT: E 421 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: E 456 TRP cc_start: 0.6538 (t60) cc_final: 0.5357 (t-100) outliers start: 48 outliers final: 30 residues processed: 162 average time/residue: 1.1490 time to fit residues: 210.8108 Evaluate side-chains 161 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 122 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 259 LEU 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 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 PHE 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 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 C 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17085 Z= 0.252 Angle : 0.871 21.464 23365 Z= 0.347 Chirality : 0.126 2.790 2775 Planarity : 0.004 0.036 2820 Dihedral : 11.723 143.020 2887 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.60 % Allowed : 14.20 % 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: 2.91 (0.18), residues: 740 sheet: -1.30 (0.22), residues: 480 loop : -0.20 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 68 HIS 0.002 0.000 HIS A 502 PHE 0.028 0.001 PHE A 199 TYR 0.014 0.001 TYR E 262 ARG 0.008 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 155 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 113 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8530 (t0) cc_final: 0.8002 (t0) REVERT: A 108 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7977 (mtpp) REVERT: A 144 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7461 (m-80) REVERT: A 291 MET cc_start: 0.6492 (tpp) cc_final: 0.5720 (ttt) REVERT: A 416 ARG cc_start: 0.6499 (mtp180) cc_final: 0.6046 (mmp-170) REVERT: A 421 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: A 456 TRP cc_start: 0.6612 (t60) cc_final: 0.5263 (t-100) REVERT: D 52 ASP cc_start: 0.7625 (t0) cc_final: 0.7124 (t0) REVERT: D 416 ARG cc_start: 0.6319 (mtp180) cc_final: 0.6054 (mmp-170) REVERT: D 421 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: D 456 TRP cc_start: 0.6658 (t60) cc_final: 0.5308 (t-100) REVERT: B 52 ASP cc_start: 0.7624 (t0) cc_final: 0.7311 (t70) REVERT: B 105 ASP cc_start: 0.8598 (t0) cc_final: 0.8237 (t0) REVERT: B 250 GLU cc_start: 0.7433 (pt0) cc_final: 0.7231 (pt0) REVERT: B 416 ARG cc_start: 0.6337 (mtp180) cc_final: 0.5954 (mmp-170) REVERT: B 421 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: B 456 TRP cc_start: 0.6659 (t60) cc_final: 0.5310 (t-100) REVERT: C 108 LYS cc_start: 0.8329 (mtmp) cc_final: 0.7957 (mtpp) REVERT: C 199 PHE cc_start: 0.7715 (t80) cc_final: 0.7458 (t80) REVERT: C 416 ARG cc_start: 0.6241 (mtp180) cc_final: 0.5903 (mmp-170) REVERT: C 421 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6046 (tt0) REVERT: C 456 TRP cc_start: 0.6795 (t60) cc_final: 0.5675 (t-100) REVERT: E 45 MET cc_start: 0.8703 (mmm) cc_final: 0.8068 (tpt) REVERT: E 52 ASP cc_start: 0.7649 (t0) cc_final: 0.6665 (t0) REVERT: E 416 ARG cc_start: 0.6293 (mtp180) cc_final: 0.5869 (mmp-170) REVERT: E 421 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6450 (tt0) REVERT: E 456 TRP cc_start: 0.6631 (t60) cc_final: 0.5415 (t-100) outliers start: 42 outliers final: 34 residues processed: 147 average time/residue: 1.2341 time to fit residues: 203.8562 Evaluate side-chains 155 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 259 LEU 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 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 PHE 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 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 421 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 314 GLN B 314 GLN C 22 ASN C 314 GLN E 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17085 Z= 0.204 Angle : 0.860 21.528 23365 Z= 0.341 Chirality : 0.126 2.790 2775 Planarity : 0.004 0.038 2820 Dihedral : 11.680 142.896 2887 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.60 % Allowed : 14.25 % 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: 1.10 (0.20), residues: 1930 helix: 2.97 (0.18), residues: 740 sheet: -1.26 (0.22), residues: 475 loop : -0.17 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS A 502 PHE 0.021 0.001 PHE A 199 TYR 0.015 0.001 TYR B 262 ARG 0.008 0.000 ARG A 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 158 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8524 (t0) cc_final: 0.7995 (t0) REVERT: A 108 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7960 (mtpp) REVERT: A 291 MET cc_start: 0.6442 (tpp) cc_final: 0.5673 (ttt) REVERT: A 416 ARG cc_start: 0.6464 (mtp180) cc_final: 0.6014 (mmp-170) REVERT: A 421 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: A 456 TRP cc_start: 0.6624 (t60) cc_final: 0.5281 (t-100) REVERT: D 52 ASP cc_start: 0.7605 (t0) cc_final: 0.7105 (t0) REVERT: D 291 MET cc_start: 0.7111 (tpp) cc_final: 0.5899 (ttt) REVERT: D 416 ARG cc_start: 0.6311 (mtp180) cc_final: 0.6049 (mmp-170) REVERT: D 421 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: D 456 TRP cc_start: 0.6539 (t60) cc_final: 0.5187 (t-100) REVERT: B 52 ASP cc_start: 0.7606 (t0) cc_final: 0.7293 (t70) REVERT: B 105 ASP cc_start: 0.8613 (t0) cc_final: 0.8243 (t0) REVERT: B 416 ARG cc_start: 0.6335 (mtp180) cc_final: 0.5950 (mmp-170) REVERT: B 421 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6437 (tt0) REVERT: B 456 TRP cc_start: 0.6645 (t60) cc_final: 0.5297 (t-100) REVERT: C 108 LYS cc_start: 0.8321 (mtmp) cc_final: 0.7933 (mtpp) REVERT: C 199 PHE cc_start: 0.7725 (t80) cc_final: 0.7470 (t80) REVERT: C 416 ARG cc_start: 0.6235 (mtp180) cc_final: 0.5897 (mmp-170) REVERT: C 421 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6006 (tt0) REVERT: C 456 TRP cc_start: 0.6769 (t60) cc_final: 0.5641 (t-100) REVERT: E 45 MET cc_start: 0.8687 (mmm) cc_final: 0.7906 (tpt) REVERT: E 52 ASP cc_start: 0.7629 (t0) cc_final: 0.6674 (t0) REVERT: E 416 ARG cc_start: 0.6286 (mtp180) cc_final: 0.5862 (mmp-170) REVERT: E 421 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: E 456 TRP cc_start: 0.6668 (t60) cc_final: 0.5414 (t-100) outliers start: 42 outliers final: 35 residues processed: 148 average time/residue: 1.2113 time to fit residues: 201.3813 Evaluate side-chains 153 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 113 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 259 LEU 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 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 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 242 PHE 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 41 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 421 GLU 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 46 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 155 optimal weight: 0.4980 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 22 ASN D 314 GLN B 314 GLN C 22 ASN C 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.086118 restraints weight = 77816.701| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.14 r_work: 0.2829 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17085 Z= 0.173 Angle : 0.851 21.750 23365 Z= 0.336 Chirality : 0.125 2.782 2775 Planarity : 0.004 0.036 2820 Dihedral : 11.573 142.482 2885 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.38 % Allowed : 14.75 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.05 (0.19), residues: 740 sheet: -1.22 (0.22), residues: 475 loop : -0.06 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 68 HIS 0.001 0.000 HIS A 502 PHE 0.022 0.001 PHE A 199 TYR 0.014 0.001 TYR B 262 ARG 0.008 0.000 ARG C 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4754.67 seconds wall clock time: 86 minutes 12.43 seconds (5172.43 seconds total)