Starting phenix.real_space_refine on Fri Feb 16 08:53:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/02_2024/5vms_8712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/02_2024/5vms_8712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/02_2024/5vms_8712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/02_2024/5vms_8712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/02_2024/5vms_8712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/02_2024/5vms_8712.pdb" } resolution = 3.7 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= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 64 5.16 5 C 9708 2.51 5 N 2588 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 227": "NH1" <-> "NH2" Residue "G ARG 233": "NH1" <-> "NH2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "G ARG 500": "NH1" <-> "NH2" Residue "G TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 528": "NH1" <-> "NH2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 75": "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: 14916 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2717 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1012 Unusual residues: {' CA': 3} Classifications: {'peptide': 141, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 138, None: 3} Not linked: pdbres="MET B 146 " pdbres=" CA B 201 " Not linked: pdbres=" CA B 201 " pdbres=" CA B 202 " Not linked: pdbres=" CA B 202 " pdbres=" CA B 203 " Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2717 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1012 Unusual residues: {' CA': 3} Classifications: {'peptide': 141, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 138, None: 3} Not linked: pdbres="MET D 146 " pdbres=" CA D 201 " Not linked: pdbres=" CA D 201 " pdbres=" CA D 202 " Not linked: pdbres=" CA D 202 " pdbres=" CA D 203 " Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2717 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1012 Unusual residues: {' CA': 3} Classifications: {'peptide': 141, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 138, None: 3} Not linked: pdbres="MET F 146 " pdbres=" CA F 201 " Not linked: pdbres=" CA F 201 " pdbres=" CA F 202 " Not linked: pdbres=" CA F 202 " pdbres=" CA F 203 " Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2717 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1012 Unusual residues: {' CA': 3} Classifications: {'peptide': 141, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 138, None: 3} Not linked: pdbres="MET H 146 " pdbres=" CA H 201 " Not linked: pdbres=" CA H 201 " pdbres=" CA H 202 " Not linked: pdbres=" CA H 202 " pdbres=" CA H 203 " Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 89 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 Time building chain proxies: 8.12, per 1000 atoms: 0.54 Number of scatterers: 14916 At special positions: 0 Unit cell: (107.9, 107.9, 123.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 64 16.00 O 2544 8.00 N 2588 7.00 C 9708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 3.0 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 109 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 Processing helix chain 'A' and resid 526 through 556 Processing helix chain 'B' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 109 through 135 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 152 " --> pdb=" O TRP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 Processing helix chain 'C' and resid 526 through 556 Processing helix chain 'D' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 109 through 135 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 152 " --> pdb=" O TRP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 206 Processing helix chain 'E' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR E 254 " --> pdb=" O GLN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 302 Processing helix chain 'E' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 Processing helix chain 'E' and resid 526 through 556 Processing helix chain 'F' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 146 Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 109 through 135 Processing helix chain 'G' and resid 136 through 138 No H-bonds generated for 'chain 'G' and resid 136 through 138' Processing helix chain 'G' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL G 152 " --> pdb=" O TRP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 206 Processing helix chain 'G' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'G' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR G 254 " --> pdb=" O GLN G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 302 Processing helix chain 'G' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE G 325 " --> pdb=" O CYS G 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Proline residue: G 333 - end of helix Processing helix chain 'G' and resid 353 through 355 No H-bonds generated for 'chain 'G' and resid 353 through 355' Processing helix chain 'G' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA G 360 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN G 376 " --> pdb=" O TYR G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 523 Processing helix chain 'G' and resid 526 through 556 Processing helix chain 'H' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 146 1112 hydrogen bonds defined for protein. 3336 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: 4.22 Time building geometry restraints manager: 6.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2476 1.33 - 1.45: 4192 1.45 - 1.57: 8440 1.57 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 15228 Sorted by residual: bond pdb=" C LEU E 332 " pdb=" O LEU E 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU A 332 " pdb=" O LEU A 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU C 332 " pdb=" O LEU C 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU G 332 " pdb=" O LEU G 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C ILE C 264 " pdb=" O ILE C 264 " ideal model delta sigma weight residual 1.237 1.270 -0.033 1.13e-02 7.83e+03 8.52e+00 ... (remaining 15223 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 396 107.47 - 114.10: 8360 114.10 - 120.73: 5904 120.73 - 127.36: 5848 127.36 - 133.99: 136 Bond angle restraints: 20644 Sorted by residual: angle pdb=" N ILE E 303 " pdb=" CA ILE E 303 " pdb=" C ILE E 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE G 303 " pdb=" CA ILE G 303 " pdb=" C ILE G 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE C 303 " pdb=" CA ILE C 303 " pdb=" C ILE C 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE A 303 " pdb=" CA ILE A 303 " pdb=" C ILE A 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ASP F 21 " pdb=" CA ASP F 21 " pdb=" C ASP F 21 " ideal model delta sigma weight residual 111.33 117.80 -6.47 1.21e+00 6.83e-01 2.86e+01 ... (remaining 20639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.79: 7524 12.79 - 25.59: 1012 25.59 - 38.38: 228 38.38 - 51.17: 64 51.17 - 63.96: 20 Dihedral angle restraints: 8848 sinusoidal: 3260 harmonic: 5588 Sorted by residual: dihedral pdb=" CA SER C 323 " pdb=" C SER C 323 " pdb=" N VAL C 324 " pdb=" CA VAL C 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER A 323 " pdb=" C SER A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 323 " pdb=" C SER G 323 " pdb=" N VAL G 324 " pdb=" CA VAL G 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 8845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1764 0.071 - 0.143: 440 0.143 - 0.214: 128 0.214 - 0.285: 28 0.285 - 0.357: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA LEU G 332 " pdb=" N LEU G 332 " pdb=" C LEU G 332 " pdb=" CB LEU G 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU A 332 " pdb=" N LEU A 332 " pdb=" C LEU A 332 " pdb=" CB LEU A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU C 332 " pdb=" N LEU C 332 " pdb=" C LEU C 332 " pdb=" CB LEU C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2365 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 66 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO B 67 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 67 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 66 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 67 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.035 5.00e-02 4.00e+02 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 560 2.77 - 3.30: 17496 3.30 - 3.83: 25306 3.83 - 4.37: 26534 4.37 - 4.90: 43930 Nonbonded interactions: 113826 Sorted by model distance: nonbonded pdb=" O THR F 63 " pdb="CA CA F 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR H 63 " pdb="CA CA H 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR B 63 " pdb="CA CA B 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR D 63 " pdb="CA CA D 202 " model vdw 2.234 2.510 nonbonded pdb=" OE1 GLN E 549 " pdb=" CD1 LEU G 548 " model vdw 2.236 3.460 ... (remaining 113821 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 4.240 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.290 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.007 0.043 15228 Z= 0.488 Angle : 1.474 6.833 20644 Z= 1.155 Chirality : 0.074 0.357 2368 Planarity : 0.005 0.063 2576 Dihedral : 12.688 63.961 5248 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.67 % 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: 2.06 (0.16), residues: 1904 helix: 2.39 (0.10), residues: 1472 sheet: None (None), residues: 0 loop : -2.54 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 369 HIS 0.005 0.001 HIS E 116 PHE 0.019 0.002 PHE G 330 TYR 0.016 0.002 TYR G 534 ARG 0.003 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 896 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8035 (tp) cc_final: 0.7812 (tt) REVERT: A 153 LEU cc_start: 0.9398 (tp) cc_final: 0.9176 (tp) REVERT: A 160 GLU cc_start: 0.9549 (tt0) cc_final: 0.9213 (tt0) REVERT: A 180 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7701 (mmt-90) REVERT: A 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8074 (m-30) REVERT: A 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8597 (mttm) REVERT: A 358 ILE cc_start: 0.8879 (mt) cc_final: 0.8571 (mt) REVERT: A 499 HIS cc_start: 0.7998 (m-70) cc_final: 0.7671 (p90) REVERT: A 526 ASP cc_start: 0.8839 (t70) cc_final: 0.8448 (t70) REVERT: A 534 TYR cc_start: 0.8879 (t80) cc_final: 0.7769 (t80) REVERT: A 551 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8396 (tpt90) REVERT: B 37 MET cc_start: 0.9455 (mmm) cc_final: 0.9206 (mmm) REVERT: B 39 SER cc_start: 0.9561 (t) cc_final: 0.9307 (p) REVERT: B 45 THR cc_start: 0.8969 (m) cc_final: 0.8663 (t) REVERT: B 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9002 (mtp) REVERT: B 80 THR cc_start: 0.8229 (p) cc_final: 0.8011 (p) REVERT: B 93 PHE cc_start: 0.8231 (m-80) cc_final: 0.7882 (m-80) REVERT: B 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9245 (ttp) REVERT: B 142 PHE cc_start: 0.8570 (t80) cc_final: 0.8328 (t80) REVERT: C 141 LEU cc_start: 0.8035 (tp) cc_final: 0.7812 (tt) REVERT: C 153 LEU cc_start: 0.9400 (tp) cc_final: 0.9177 (tp) REVERT: C 160 GLU cc_start: 0.9549 (tt0) cc_final: 0.9214 (tt0) REVERT: C 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7703 (mmt-90) REVERT: C 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8075 (m-30) REVERT: C 308 LYS cc_start: 0.8847 (mttt) cc_final: 0.8595 (mttm) REVERT: C 358 ILE cc_start: 0.8878 (mt) cc_final: 0.8570 (mt) REVERT: C 499 HIS cc_start: 0.7998 (m-70) cc_final: 0.7670 (p90) REVERT: C 526 ASP cc_start: 0.8837 (t70) cc_final: 0.8446 (t70) REVERT: C 534 TYR cc_start: 0.8878 (t80) cc_final: 0.7768 (t80) REVERT: C 550 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8959 (mtp-110) REVERT: D 37 MET cc_start: 0.9454 (mmm) cc_final: 0.9206 (mmm) REVERT: D 39 SER cc_start: 0.9561 (t) cc_final: 0.9306 (p) REVERT: D 45 THR cc_start: 0.8971 (m) cc_final: 0.8665 (t) REVERT: D 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9001 (mtp) REVERT: D 80 THR cc_start: 0.8229 (p) cc_final: 0.8012 (p) REVERT: D 93 PHE cc_start: 0.8230 (m-80) cc_final: 0.7880 (m-80) REVERT: D 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9244 (ttp) REVERT: D 142 PHE cc_start: 0.8568 (t80) cc_final: 0.8328 (t80) REVERT: E 141 LEU cc_start: 0.8034 (tp) cc_final: 0.7811 (tt) REVERT: E 153 LEU cc_start: 0.9399 (tp) cc_final: 0.9177 (tp) REVERT: E 160 GLU cc_start: 0.9550 (tt0) cc_final: 0.9214 (tt0) REVERT: E 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7703 (mmt-90) REVERT: E 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8075 (m-30) REVERT: E 308 LYS cc_start: 0.8848 (mttt) cc_final: 0.8595 (mttm) REVERT: E 358 ILE cc_start: 0.8877 (mt) cc_final: 0.8568 (mt) REVERT: E 499 HIS cc_start: 0.7999 (m-70) cc_final: 0.7671 (p90) REVERT: E 526 ASP cc_start: 0.8838 (t70) cc_final: 0.8446 (t70) REVERT: E 534 TYR cc_start: 0.8876 (t80) cc_final: 0.7768 (t80) REVERT: E 550 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8960 (mtp-110) REVERT: F 37 MET cc_start: 0.9455 (mmm) cc_final: 0.9207 (mmm) REVERT: F 39 SER cc_start: 0.9560 (t) cc_final: 0.9306 (p) REVERT: F 45 THR cc_start: 0.8970 (m) cc_final: 0.8663 (t) REVERT: F 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9001 (mtp) REVERT: F 80 THR cc_start: 0.8228 (p) cc_final: 0.8010 (p) REVERT: F 93 PHE cc_start: 0.8230 (m-80) cc_final: 0.7879 (m-80) REVERT: F 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9244 (ttp) REVERT: F 142 PHE cc_start: 0.8569 (t80) cc_final: 0.8329 (t80) REVERT: G 141 LEU cc_start: 0.8034 (tp) cc_final: 0.7811 (tt) REVERT: G 153 LEU cc_start: 0.9398 (tp) cc_final: 0.9175 (tp) REVERT: G 160 GLU cc_start: 0.9550 (tt0) cc_final: 0.9213 (tt0) REVERT: G 180 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7702 (mmt-90) REVERT: G 291 ASP cc_start: 0.8332 (m-30) cc_final: 0.8074 (m-30) REVERT: G 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8597 (mttm) REVERT: G 358 ILE cc_start: 0.8878 (mt) cc_final: 0.8570 (mt) REVERT: G 499 HIS cc_start: 0.8000 (m-70) cc_final: 0.7672 (p90) REVERT: G 526 ASP cc_start: 0.8838 (t70) cc_final: 0.8447 (t70) REVERT: G 534 TYR cc_start: 0.8877 (t80) cc_final: 0.7767 (t80) REVERT: H 37 MET cc_start: 0.9456 (mmm) cc_final: 0.9206 (mmm) REVERT: H 39 SER cc_start: 0.9561 (t) cc_final: 0.9306 (p) REVERT: H 45 THR cc_start: 0.8970 (m) cc_final: 0.8665 (t) REVERT: H 52 MET cc_start: 0.9424 (mtm) cc_final: 0.9003 (mtp) REVERT: H 80 THR cc_start: 0.8228 (p) cc_final: 0.8009 (p) REVERT: H 93 PHE cc_start: 0.8231 (m-80) cc_final: 0.7881 (m-80) REVERT: H 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9245 (ttp) REVERT: H 142 PHE cc_start: 0.8569 (t80) cc_final: 0.8327 (t80) outliers start: 0 outliers final: 0 residues processed: 896 average time/residue: 0.2540 time to fit residues: 335.0303 Evaluate side-chains 692 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 357 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN E 357 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 357 GLN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15228 Z= 0.212 Angle : 0.602 6.444 20644 Z= 0.321 Chirality : 0.041 0.245 2368 Planarity : 0.004 0.041 2576 Dihedral : 3.935 22.475 2104 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 6.22 % Allowed : 16.09 % Favored : 77.69 % 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: 4.12 (0.20), residues: 1904 helix: 3.82 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.78 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 166 HIS 0.007 0.001 HIS F 108 PHE 0.028 0.002 PHE E 260 TYR 0.025 0.002 TYR E 268 ARG 0.009 0.001 ARG H 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 697 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8160 (t60) cc_final: 0.7778 (t60) REVERT: A 180 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7807 (mpt-90) REVERT: A 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8146 (m-30) REVERT: A 308 LYS cc_start: 0.8871 (mttt) cc_final: 0.8624 (mmtp) REVERT: A 498 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8429 (p-80) REVERT: A 499 HIS cc_start: 0.8323 (m-70) cc_final: 0.7972 (p-80) REVERT: A 522 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8609 (mmm-85) REVERT: A 526 ASP cc_start: 0.8981 (t70) cc_final: 0.8316 (t70) REVERT: A 534 TYR cc_start: 0.9074 (t80) cc_final: 0.8857 (t80) REVERT: A 551 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8181 (tpt170) REVERT: B 9 GLN cc_start: 0.8829 (mp10) cc_final: 0.8362 (pt0) REVERT: B 12 GLU cc_start: 0.9467 (tp30) cc_final: 0.9239 (mm-30) REVERT: B 39 SER cc_start: 0.9468 (t) cc_final: 0.9266 (p) REVERT: B 52 MET cc_start: 0.9221 (mtm) cc_final: 0.9018 (mtp) REVERT: B 117 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8528 (mt) REVERT: B 121 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8503 (mm-30) REVERT: B 125 MET cc_start: 0.9590 (ttt) cc_final: 0.9373 (ttp) REVERT: C 166 TRP cc_start: 0.8160 (t60) cc_final: 0.7779 (t60) REVERT: C 180 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7807 (mpt-90) REVERT: C 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8146 (m-30) REVERT: C 308 LYS cc_start: 0.8871 (mttt) cc_final: 0.8624 (mmtp) REVERT: C 498 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8430 (p-80) REVERT: C 499 HIS cc_start: 0.8323 (m-70) cc_final: 0.7972 (p-80) REVERT: C 522 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8607 (mmm-85) REVERT: C 526 ASP cc_start: 0.8978 (t70) cc_final: 0.8315 (t70) REVERT: C 534 TYR cc_start: 0.9074 (t80) cc_final: 0.8858 (t80) REVERT: D 9 GLN cc_start: 0.8829 (mp10) cc_final: 0.8363 (pt0) REVERT: D 12 GLU cc_start: 0.9467 (tp30) cc_final: 0.9239 (mm-30) REVERT: D 39 SER cc_start: 0.9468 (t) cc_final: 0.9265 (p) REVERT: D 52 MET cc_start: 0.9222 (mtm) cc_final: 0.9018 (mtp) REVERT: D 117 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8530 (mt) REVERT: D 121 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8504 (mm-30) REVERT: D 125 MET cc_start: 0.9589 (ttt) cc_final: 0.9373 (ttp) REVERT: E 166 TRP cc_start: 0.8159 (t60) cc_final: 0.7778 (t60) REVERT: E 180 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7807 (mpt-90) REVERT: E 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8145 (m-30) REVERT: E 308 LYS cc_start: 0.8871 (mttt) cc_final: 0.8623 (mmtp) REVERT: E 498 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8429 (p-80) REVERT: E 499 HIS cc_start: 0.8322 (m-70) cc_final: 0.7972 (p-80) REVERT: E 522 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8609 (mmm-85) REVERT: E 526 ASP cc_start: 0.8980 (t70) cc_final: 0.8316 (t70) REVERT: E 534 TYR cc_start: 0.9074 (t80) cc_final: 0.8859 (t80) REVERT: E 550 ARG cc_start: 0.9059 (ttm110) cc_final: 0.8837 (mtm110) REVERT: F 9 GLN cc_start: 0.8829 (mp10) cc_final: 0.8363 (pt0) REVERT: F 12 GLU cc_start: 0.9467 (tp30) cc_final: 0.9239 (mm-30) REVERT: F 39 SER cc_start: 0.9468 (t) cc_final: 0.9265 (p) REVERT: F 52 MET cc_start: 0.9222 (mtm) cc_final: 0.9018 (mtp) REVERT: F 117 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8527 (mt) REVERT: F 121 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8502 (mm-30) REVERT: F 125 MET cc_start: 0.9590 (ttt) cc_final: 0.9373 (ttp) REVERT: G 166 TRP cc_start: 0.8160 (t60) cc_final: 0.7779 (t60) REVERT: G 180 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7806 (mpt-90) REVERT: G 291 ASP cc_start: 0.8418 (m-30) cc_final: 0.8145 (m-30) REVERT: G 308 LYS cc_start: 0.8869 (mttt) cc_final: 0.8622 (mmtp) REVERT: G 498 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (p-80) REVERT: G 499 HIS cc_start: 0.8323 (m-70) cc_final: 0.7972 (p-80) REVERT: G 522 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8608 (mmm-85) REVERT: G 526 ASP cc_start: 0.8979 (t70) cc_final: 0.8315 (t70) REVERT: G 534 TYR cc_start: 0.9073 (t80) cc_final: 0.8858 (t80) REVERT: G 549 GLN cc_start: 0.9234 (tp40) cc_final: 0.8947 (tp40) REVERT: H 9 GLN cc_start: 0.8830 (mp10) cc_final: 0.8362 (pt0) REVERT: H 12 GLU cc_start: 0.9467 (tp30) cc_final: 0.9239 (mm-30) REVERT: H 39 SER cc_start: 0.9468 (t) cc_final: 0.9265 (p) REVERT: H 52 MET cc_start: 0.9221 (mtm) cc_final: 0.9019 (mtp) REVERT: H 117 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8527 (mt) REVERT: H 121 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8503 (mm-30) REVERT: H 125 MET cc_start: 0.9590 (ttt) cc_final: 0.9373 (ttp) outliers start: 90 outliers final: 60 residues processed: 731 average time/residue: 0.2365 time to fit residues: 259.0349 Evaluate side-chains 724 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 656 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 54 ASN B 112 ASN C 366 GLN D 54 ASN D 112 ASN E 366 GLN F 54 ASN F 112 ASN G 366 GLN H 54 ASN H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15228 Z= 0.240 Angle : 0.559 6.241 20644 Z= 0.300 Chirality : 0.039 0.140 2368 Planarity : 0.004 0.031 2576 Dihedral : 3.836 21.777 2104 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 8.29 % Allowed : 18.65 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.91 (0.20), residues: 1904 helix: 3.57 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS H 108 PHE 0.020 0.002 PHE E 260 TYR 0.014 0.002 TYR F 139 ARG 0.007 0.001 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 648 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8150 (t60) cc_final: 0.7680 (t60) REVERT: A 180 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7555 (mtt-85) REVERT: A 291 ASP cc_start: 0.8263 (m-30) cc_final: 0.8063 (m-30) REVERT: A 308 LYS cc_start: 0.8908 (mttt) cc_final: 0.8654 (mttm) REVERT: A 355 ASN cc_start: 0.8430 (p0) cc_final: 0.8210 (p0) REVERT: A 499 HIS cc_start: 0.8266 (m-70) cc_final: 0.7941 (p-80) REVERT: A 526 ASP cc_start: 0.9007 (t70) cc_final: 0.8316 (t70) REVERT: B 9 GLN cc_start: 0.8797 (mp10) cc_final: 0.8389 (pt0) REVERT: B 12 GLU cc_start: 0.9470 (tp30) cc_final: 0.9228 (mm-30) REVERT: B 39 SER cc_start: 0.9551 (t) cc_final: 0.9270 (p) REVERT: B 46 GLU cc_start: 0.9011 (tp30) cc_final: 0.8746 (tp30) REVERT: B 52 MET cc_start: 0.9293 (mtm) cc_final: 0.8984 (mtp) REVERT: B 54 ASN cc_start: 0.9283 (m-40) cc_final: 0.8981 (m110) REVERT: B 72 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8618 (mtm) REVERT: B 115 GLU cc_start: 0.8586 (mp0) cc_final: 0.8240 (mp0) REVERT: B 117 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 120 GLU cc_start: 0.9233 (tp30) cc_final: 0.8916 (mm-30) REVERT: B 125 MET cc_start: 0.9615 (ttt) cc_final: 0.9322 (ttt) REVERT: C 166 TRP cc_start: 0.8151 (t60) cc_final: 0.7682 (t60) REVERT: C 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7559 (mtt-85) REVERT: C 291 ASP cc_start: 0.8264 (m-30) cc_final: 0.8063 (m-30) REVERT: C 308 LYS cc_start: 0.8907 (mttt) cc_final: 0.8658 (mttm) REVERT: C 499 HIS cc_start: 0.8265 (m-70) cc_final: 0.7941 (p-80) REVERT: C 526 ASP cc_start: 0.9007 (t70) cc_final: 0.8316 (t70) REVERT: D 9 GLN cc_start: 0.8797 (mp10) cc_final: 0.8389 (pt0) REVERT: D 12 GLU cc_start: 0.9470 (tp30) cc_final: 0.9228 (mm-30) REVERT: D 39 SER cc_start: 0.9550 (t) cc_final: 0.9269 (p) REVERT: D 46 GLU cc_start: 0.9010 (tp30) cc_final: 0.8745 (tp30) REVERT: D 52 MET cc_start: 0.9292 (mtm) cc_final: 0.8983 (mtp) REVERT: D 54 ASN cc_start: 0.9283 (m-40) cc_final: 0.8980 (m110) REVERT: D 72 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8619 (mtm) REVERT: D 115 GLU cc_start: 0.8587 (mp0) cc_final: 0.8243 (mp0) REVERT: D 117 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8642 (mt) REVERT: D 120 GLU cc_start: 0.9233 (tp30) cc_final: 0.8916 (mm-30) REVERT: D 125 MET cc_start: 0.9615 (ttt) cc_final: 0.9322 (ttt) REVERT: E 166 TRP cc_start: 0.8151 (t60) cc_final: 0.7681 (t60) REVERT: E 180 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7557 (mtt-85) REVERT: E 291 ASP cc_start: 0.8265 (m-30) cc_final: 0.8064 (m-30) REVERT: E 308 LYS cc_start: 0.8906 (mttt) cc_final: 0.8653 (mttm) REVERT: E 355 ASN cc_start: 0.8432 (p0) cc_final: 0.8230 (p0) REVERT: E 499 HIS cc_start: 0.8264 (m-70) cc_final: 0.7940 (p-80) REVERT: E 526 ASP cc_start: 0.9007 (t70) cc_final: 0.8318 (t70) REVERT: E 533 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8821 (tm-30) REVERT: E 550 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8823 (mtm110) REVERT: F 9 GLN cc_start: 0.8798 (mp10) cc_final: 0.8390 (pt0) REVERT: F 12 GLU cc_start: 0.9470 (tp30) cc_final: 0.9228 (mm-30) REVERT: F 39 SER cc_start: 0.9550 (t) cc_final: 0.9269 (p) REVERT: F 46 GLU cc_start: 0.9010 (tp30) cc_final: 0.8745 (tp30) REVERT: F 52 MET cc_start: 0.9292 (mtm) cc_final: 0.8983 (mtp) REVERT: F 54 ASN cc_start: 0.9283 (m-40) cc_final: 0.8981 (m110) REVERT: F 72 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8619 (mtm) REVERT: F 115 GLU cc_start: 0.8588 (mp0) cc_final: 0.8243 (mp0) REVERT: F 117 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8644 (mt) REVERT: F 120 GLU cc_start: 0.9233 (tp30) cc_final: 0.8917 (mm-30) REVERT: F 125 MET cc_start: 0.9615 (ttt) cc_final: 0.9322 (ttt) REVERT: G 166 TRP cc_start: 0.8150 (t60) cc_final: 0.7682 (t60) REVERT: G 180 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7558 (mtt-85) REVERT: G 291 ASP cc_start: 0.8264 (m-30) cc_final: 0.8062 (m-30) REVERT: G 308 LYS cc_start: 0.8908 (mttt) cc_final: 0.8657 (mttm) REVERT: G 355 ASN cc_start: 0.8429 (p0) cc_final: 0.8209 (p0) REVERT: G 499 HIS cc_start: 0.8264 (m-70) cc_final: 0.7941 (p-80) REVERT: G 526 ASP cc_start: 0.9009 (t70) cc_final: 0.8316 (t70) REVERT: H 9 GLN cc_start: 0.8798 (mp10) cc_final: 0.8389 (pt0) REVERT: H 12 GLU cc_start: 0.9470 (tp30) cc_final: 0.9229 (mm-30) REVERT: H 39 SER cc_start: 0.9550 (t) cc_final: 0.9269 (p) REVERT: H 46 GLU cc_start: 0.9010 (tp30) cc_final: 0.8746 (tp30) REVERT: H 52 MET cc_start: 0.9293 (mtm) cc_final: 0.8984 (mtp) REVERT: H 54 ASN cc_start: 0.9284 (m-40) cc_final: 0.8981 (m110) REVERT: H 72 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8617 (mtm) REVERT: H 115 GLU cc_start: 0.8586 (mp0) cc_final: 0.8241 (mp0) REVERT: H 117 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8644 (mt) REVERT: H 120 GLU cc_start: 0.9234 (tp30) cc_final: 0.8917 (mm-30) REVERT: H 125 MET cc_start: 0.9614 (ttt) cc_final: 0.9322 (ttt) outliers start: 120 outliers final: 90 residues processed: 682 average time/residue: 0.2280 time to fit residues: 237.5059 Evaluate side-chains 728 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 630 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15228 Z= 0.245 Angle : 0.562 7.232 20644 Z= 0.294 Chirality : 0.039 0.235 2368 Planarity : 0.004 0.030 2576 Dihedral : 3.752 20.799 2104 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.18 % Allowed : 22.79 % Favored : 70.03 % 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: 3.78 (0.20), residues: 1904 helix: 3.39 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 369 HIS 0.005 0.001 HIS H 108 PHE 0.019 0.002 PHE C 260 TYR 0.019 0.002 TYR E 268 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 653 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8112 (t60) cc_final: 0.7683 (t60) REVERT: A 180 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7586 (mtt-85) REVERT: A 227 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7729 (ttp80) REVERT: A 308 LYS cc_start: 0.8841 (mttt) cc_final: 0.8615 (mttm) REVERT: A 355 ASN cc_start: 0.8619 (p0) cc_final: 0.8326 (p0) REVERT: A 499 HIS cc_start: 0.8188 (m-70) cc_final: 0.7890 (p-80) REVERT: A 526 ASP cc_start: 0.9048 (t70) cc_final: 0.8357 (t70) REVERT: A 533 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8849 (tm-30) REVERT: B 12 GLU cc_start: 0.9477 (tp30) cc_final: 0.9220 (mm-30) REVERT: B 39 SER cc_start: 0.9533 (t) cc_final: 0.9263 (p) REVERT: B 46 GLU cc_start: 0.8969 (tp30) cc_final: 0.8705 (tp30) REVERT: B 52 MET cc_start: 0.9312 (mtm) cc_final: 0.9041 (mtp) REVERT: B 54 ASN cc_start: 0.9039 (m-40) cc_final: 0.8809 (m110) REVERT: B 115 GLU cc_start: 0.8794 (mp0) cc_final: 0.8593 (mp0) REVERT: B 117 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 121 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8473 (mm-30) REVERT: B 125 MET cc_start: 0.9608 (ttt) cc_final: 0.9320 (ttt) REVERT: B 127 ARG cc_start: 0.9155 (ttp-110) cc_final: 0.8726 (mtm-85) REVERT: C 166 TRP cc_start: 0.8154 (t60) cc_final: 0.7638 (t60) REVERT: C 180 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7565 (mmt-90) REVERT: C 227 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7723 (ttp80) REVERT: C 308 LYS cc_start: 0.8836 (mttt) cc_final: 0.8614 (mttm) REVERT: C 499 HIS cc_start: 0.8189 (m-70) cc_final: 0.7891 (p-80) REVERT: C 526 ASP cc_start: 0.9046 (t70) cc_final: 0.8357 (t70) REVERT: C 533 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8817 (tm-30) REVERT: D 12 GLU cc_start: 0.9477 (tp30) cc_final: 0.9221 (mm-30) REVERT: D 39 SER cc_start: 0.9533 (t) cc_final: 0.9263 (p) REVERT: D 46 GLU cc_start: 0.8970 (tp30) cc_final: 0.8706 (tp30) REVERT: D 52 MET cc_start: 0.9313 (mtm) cc_final: 0.9042 (mtp) REVERT: D 54 ASN cc_start: 0.9041 (m-40) cc_final: 0.8810 (m110) REVERT: D 115 GLU cc_start: 0.8794 (mp0) cc_final: 0.8594 (mp0) REVERT: D 117 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8425 (mt) REVERT: D 121 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8472 (mm-30) REVERT: D 125 MET cc_start: 0.9607 (ttt) cc_final: 0.9319 (ttt) REVERT: D 127 ARG cc_start: 0.9166 (ttp-110) cc_final: 0.8749 (mtm-85) REVERT: E 166 TRP cc_start: 0.8112 (t60) cc_final: 0.7684 (t60) REVERT: E 180 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7586 (mtt-85) REVERT: E 227 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7728 (ttp80) REVERT: E 308 LYS cc_start: 0.8838 (mttt) cc_final: 0.8613 (mttm) REVERT: E 355 ASN cc_start: 0.8621 (p0) cc_final: 0.8326 (p0) REVERT: E 499 HIS cc_start: 0.8190 (m-70) cc_final: 0.7891 (p-80) REVERT: E 526 ASP cc_start: 0.9048 (t70) cc_final: 0.8359 (t70) REVERT: E 533 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8818 (tm-30) REVERT: E 550 ARG cc_start: 0.8930 (ttm110) cc_final: 0.8677 (mtp-110) REVERT: F 12 GLU cc_start: 0.9476 (tp30) cc_final: 0.9220 (mm-30) REVERT: F 39 SER cc_start: 0.9533 (t) cc_final: 0.9263 (p) REVERT: F 46 GLU cc_start: 0.8969 (tp30) cc_final: 0.8705 (tp30) REVERT: F 52 MET cc_start: 0.9313 (mtm) cc_final: 0.9043 (mtp) REVERT: F 54 ASN cc_start: 0.9041 (m-40) cc_final: 0.8810 (m110) REVERT: F 115 GLU cc_start: 0.8794 (mp0) cc_final: 0.8594 (mp0) REVERT: F 117 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8426 (mt) REVERT: F 121 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8474 (mm-30) REVERT: F 125 MET cc_start: 0.9606 (ttt) cc_final: 0.9319 (ttt) REVERT: F 127 ARG cc_start: 0.9155 (ttp-110) cc_final: 0.8725 (mtm-85) REVERT: G 166 TRP cc_start: 0.8153 (t60) cc_final: 0.7638 (t60) REVERT: G 180 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7564 (mmt-90) REVERT: G 227 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7724 (ttp80) REVERT: G 308 LYS cc_start: 0.8833 (mttt) cc_final: 0.8611 (mttm) REVERT: G 355 ASN cc_start: 0.8620 (p0) cc_final: 0.8326 (p0) REVERT: G 499 HIS cc_start: 0.8191 (m-70) cc_final: 0.7892 (p-80) REVERT: G 526 ASP cc_start: 0.9049 (t70) cc_final: 0.8358 (t70) REVERT: G 533 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8819 (tm-30) REVERT: H 12 GLU cc_start: 0.9476 (tp30) cc_final: 0.9220 (mm-30) REVERT: H 39 SER cc_start: 0.9533 (t) cc_final: 0.9263 (p) REVERT: H 46 GLU cc_start: 0.8970 (tp30) cc_final: 0.8706 (tp30) REVERT: H 52 MET cc_start: 0.9312 (mtm) cc_final: 0.9043 (mtp) REVERT: H 54 ASN cc_start: 0.9040 (m-40) cc_final: 0.8809 (m110) REVERT: H 115 GLU cc_start: 0.8793 (mp0) cc_final: 0.8593 (mp0) REVERT: H 117 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8427 (mt) REVERT: H 121 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8474 (mm-30) REVERT: H 125 MET cc_start: 0.9607 (ttt) cc_final: 0.9319 (ttt) REVERT: H 127 ARG cc_start: 0.9156 (ttp-110) cc_final: 0.8725 (mtm-85) outliers start: 104 outliers final: 83 residues processed: 686 average time/residue: 0.2379 time to fit residues: 246.2501 Evaluate side-chains 714 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 623 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15228 Z= 0.282 Angle : 0.566 7.023 20644 Z= 0.300 Chirality : 0.038 0.155 2368 Planarity : 0.004 0.057 2576 Dihedral : 3.728 18.205 2104 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 8.91 % Allowed : 21.27 % Favored : 69.82 % 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: 3.52 (0.20), residues: 1904 helix: 3.11 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 369 HIS 0.005 0.001 HIS D 108 PHE 0.016 0.002 PHE E 260 TYR 0.019 0.002 TYR E 268 ARG 0.009 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 623 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7633 (mtt-85) REVERT: A 227 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7589 (ttp80) REVERT: A 499 HIS cc_start: 0.8208 (m-70) cc_final: 0.7881 (p-80) REVERT: A 526 ASP cc_start: 0.9110 (t70) cc_final: 0.8481 (t70) REVERT: A 533 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8601 (tm-30) REVERT: B 12 GLU cc_start: 0.9496 (tp30) cc_final: 0.9235 (mm-30) REVERT: B 39 SER cc_start: 0.9390 (t) cc_final: 0.9148 (p) REVERT: B 46 GLU cc_start: 0.9065 (tp30) cc_final: 0.8799 (tp30) REVERT: B 52 MET cc_start: 0.9296 (mtm) cc_final: 0.9008 (mtp) REVERT: B 64 ILE cc_start: 0.9466 (mm) cc_final: 0.9239 (mm) REVERT: B 117 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (mt) REVERT: B 121 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8548 (mm-30) REVERT: B 125 MET cc_start: 0.9609 (ttt) cc_final: 0.9323 (ttt) REVERT: B 127 ARG cc_start: 0.9229 (ttp-110) cc_final: 0.8756 (mtm-85) REVERT: C 104 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8757 (tp) REVERT: C 180 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7683 (mmt90) REVERT: C 227 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7584 (ttp80) REVERT: C 499 HIS cc_start: 0.8208 (m-70) cc_final: 0.7880 (p-80) REVERT: C 526 ASP cc_start: 0.9110 (t70) cc_final: 0.8481 (t70) REVERT: C 533 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8601 (tm-30) REVERT: D 12 GLU cc_start: 0.9496 (tp30) cc_final: 0.9236 (mm-30) REVERT: D 39 SER cc_start: 0.9390 (t) cc_final: 0.9149 (p) REVERT: D 46 GLU cc_start: 0.9064 (tp30) cc_final: 0.8799 (tp30) REVERT: D 52 MET cc_start: 0.9298 (mtm) cc_final: 0.9009 (mtp) REVERT: D 64 ILE cc_start: 0.9468 (mm) cc_final: 0.9240 (mm) REVERT: D 117 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8691 (mt) REVERT: D 121 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8550 (mm-30) REVERT: D 125 MET cc_start: 0.9608 (ttt) cc_final: 0.9322 (ttt) REVERT: D 127 ARG cc_start: 0.9228 (ttp-110) cc_final: 0.8756 (mtm-85) REVERT: E 180 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7635 (mtt-85) REVERT: E 227 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7591 (ttp80) REVERT: E 355 ASN cc_start: 0.8713 (p0) cc_final: 0.8512 (p0) REVERT: E 499 HIS cc_start: 0.8208 (m-70) cc_final: 0.7881 (p-80) REVERT: E 526 ASP cc_start: 0.9111 (t70) cc_final: 0.8481 (t70) REVERT: E 533 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8601 (tm-30) REVERT: E 550 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8700 (ttp80) REVERT: F 12 GLU cc_start: 0.9496 (tp30) cc_final: 0.9235 (mm-30) REVERT: F 39 SER cc_start: 0.9389 (t) cc_final: 0.9147 (p) REVERT: F 46 GLU cc_start: 0.9066 (tp30) cc_final: 0.8800 (tp30) REVERT: F 52 MET cc_start: 0.9296 (mtm) cc_final: 0.9009 (mtp) REVERT: F 64 ILE cc_start: 0.9467 (mm) cc_final: 0.9239 (mm) REVERT: F 117 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8691 (mt) REVERT: F 121 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8549 (mm-30) REVERT: F 125 MET cc_start: 0.9609 (ttt) cc_final: 0.9323 (ttt) REVERT: F 127 ARG cc_start: 0.9228 (ttp-110) cc_final: 0.8756 (mtm-85) REVERT: G 104 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8757 (tp) REVERT: G 180 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7683 (mmt90) REVERT: G 227 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7587 (ttp80) REVERT: G 499 HIS cc_start: 0.8209 (m-70) cc_final: 0.7882 (p-80) REVERT: G 526 ASP cc_start: 0.9110 (t70) cc_final: 0.8482 (t70) REVERT: G 533 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8601 (tm-30) REVERT: H 12 GLU cc_start: 0.9496 (tp30) cc_final: 0.9235 (mm-30) REVERT: H 39 SER cc_start: 0.9390 (t) cc_final: 0.9149 (p) REVERT: H 46 GLU cc_start: 0.9066 (tp30) cc_final: 0.8801 (tp30) REVERT: H 52 MET cc_start: 0.9297 (mtm) cc_final: 0.9009 (mtp) REVERT: H 64 ILE cc_start: 0.9468 (mm) cc_final: 0.9239 (mm) REVERT: H 117 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (mt) REVERT: H 121 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8549 (mm-30) REVERT: H 125 MET cc_start: 0.9609 (ttt) cc_final: 0.9323 (ttt) REVERT: H 127 ARG cc_start: 0.9229 (ttp-110) cc_final: 0.8756 (mtm-85) outliers start: 129 outliers final: 100 residues processed: 662 average time/residue: 0.2347 time to fit residues: 234.5151 Evaluate side-chains 723 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 613 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 112 ASN D 54 ASN D 112 ASN F 54 ASN F 112 ASN H 54 ASN H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15228 Z= 0.190 Angle : 0.587 8.848 20644 Z= 0.295 Chirality : 0.038 0.161 2368 Planarity : 0.003 0.034 2576 Dihedral : 3.590 17.849 2104 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.08 % Allowed : 26.93 % Favored : 66.99 % 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: 3.62 (0.20), residues: 1904 helix: 3.25 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.98 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 369 HIS 0.005 0.001 HIS B 108 PHE 0.018 0.001 PHE G 260 TYR 0.017 0.002 TYR E 268 ARG 0.006 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 649 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8182 (t60) cc_final: 0.7717 (t60) REVERT: A 180 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7426 (mtt-85) REVERT: A 227 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7824 (ttp80) REVERT: A 499 HIS cc_start: 0.8192 (m-70) cc_final: 0.7878 (p-80) REVERT: A 526 ASP cc_start: 0.9049 (t70) cc_final: 0.8370 (t70) REVERT: A 533 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 9 GLN cc_start: 0.8741 (mp10) cc_final: 0.8250 (pt0) REVERT: B 12 GLU cc_start: 0.9498 (tp30) cc_final: 0.9229 (mm-30) REVERT: B 39 SER cc_start: 0.9360 (t) cc_final: 0.9121 (p) REVERT: B 46 GLU cc_start: 0.9036 (tp30) cc_final: 0.8770 (tp30) REVERT: B 52 MET cc_start: 0.9325 (mtm) cc_final: 0.8920 (mtm) REVERT: B 54 ASN cc_start: 0.9027 (m-40) cc_final: 0.8724 (m110) REVERT: B 117 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 120 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8966 (mm-30) REVERT: B 121 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8206 (mm-30) REVERT: B 124 GLU cc_start: 0.8982 (tp30) cc_final: 0.8720 (tp30) REVERT: B 125 MET cc_start: 0.9606 (ttt) cc_final: 0.9329 (ttt) REVERT: B 127 ARG cc_start: 0.9211 (ttp-110) cc_final: 0.8985 (ttm110) REVERT: C 104 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8753 (tp) REVERT: C 166 TRP cc_start: 0.8203 (t60) cc_final: 0.7708 (t60) REVERT: C 180 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7249 (mtt-85) REVERT: C 227 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7813 (ttp80) REVERT: C 343 LEU cc_start: 0.8978 (mt) cc_final: 0.8616 (mp) REVERT: C 499 HIS cc_start: 0.8190 (m-70) cc_final: 0.7876 (p-80) REVERT: C 526 ASP cc_start: 0.9049 (t70) cc_final: 0.8370 (t70) REVERT: C 533 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 550 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8822 (mtp-110) REVERT: D 9 GLN cc_start: 0.8741 (mp10) cc_final: 0.8250 (pt0) REVERT: D 12 GLU cc_start: 0.9498 (tp30) cc_final: 0.9230 (mm-30) REVERT: D 39 SER cc_start: 0.9360 (t) cc_final: 0.9121 (p) REVERT: D 46 GLU cc_start: 0.9036 (tp30) cc_final: 0.8771 (tp30) REVERT: D 52 MET cc_start: 0.9325 (mtm) cc_final: 0.8926 (mtm) REVERT: D 54 ASN cc_start: 0.9023 (m-40) cc_final: 0.8721 (m110) REVERT: D 117 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8392 (mt) REVERT: D 120 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8966 (mm-30) REVERT: D 121 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8208 (mm-30) REVERT: D 124 GLU cc_start: 0.8982 (tp30) cc_final: 0.8721 (tp30) REVERT: D 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9329 (ttt) REVERT: D 127 ARG cc_start: 0.9211 (ttp-110) cc_final: 0.8986 (ttm110) REVERT: E 166 TRP cc_start: 0.8183 (t60) cc_final: 0.7718 (t60) REVERT: E 180 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7428 (mtt-85) REVERT: E 227 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7824 (ttp80) REVERT: E 355 ASN cc_start: 0.8635 (p0) cc_final: 0.8404 (p0) REVERT: E 499 HIS cc_start: 0.8191 (m-70) cc_final: 0.7878 (p-80) REVERT: E 526 ASP cc_start: 0.9048 (t70) cc_final: 0.8369 (t70) REVERT: E 533 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8492 (tm-30) REVERT: F 9 GLN cc_start: 0.8741 (mp10) cc_final: 0.8249 (pt0) REVERT: F 12 GLU cc_start: 0.9498 (tp30) cc_final: 0.9229 (mm-30) REVERT: F 39 SER cc_start: 0.9359 (t) cc_final: 0.9119 (p) REVERT: F 46 GLU cc_start: 0.9037 (tp30) cc_final: 0.8772 (tp30) REVERT: F 52 MET cc_start: 0.9324 (mtm) cc_final: 0.8919 (mtm) REVERT: F 54 ASN cc_start: 0.9023 (m-40) cc_final: 0.8721 (m110) REVERT: F 117 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8395 (mt) REVERT: F 120 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8967 (mm-30) REVERT: F 121 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8206 (mm-30) REVERT: F 124 GLU cc_start: 0.8982 (tp30) cc_final: 0.8720 (tp30) REVERT: F 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9329 (ttt) REVERT: F 127 ARG cc_start: 0.9211 (ttp-110) cc_final: 0.8985 (ttm110) REVERT: G 104 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8650 (tp) REVERT: G 166 TRP cc_start: 0.8204 (t60) cc_final: 0.7707 (t60) REVERT: G 180 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7295 (mtt-85) REVERT: G 227 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7815 (ttp80) REVERT: G 343 LEU cc_start: 0.8979 (mt) cc_final: 0.8616 (mp) REVERT: G 499 HIS cc_start: 0.8192 (m-70) cc_final: 0.7878 (p-80) REVERT: G 526 ASP cc_start: 0.9049 (t70) cc_final: 0.8371 (t70) REVERT: G 533 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8494 (tm-30) REVERT: H 9 GLN cc_start: 0.8742 (mp10) cc_final: 0.8250 (pt0) REVERT: H 12 GLU cc_start: 0.9497 (tp30) cc_final: 0.9229 (mm-30) REVERT: H 39 SER cc_start: 0.9361 (t) cc_final: 0.9121 (p) REVERT: H 46 GLU cc_start: 0.9037 (tp30) cc_final: 0.8772 (tp30) REVERT: H 52 MET cc_start: 0.9324 (mtm) cc_final: 0.8919 (mtm) REVERT: H 54 ASN cc_start: 0.9022 (m-40) cc_final: 0.8721 (m110) REVERT: H 117 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8393 (mt) REVERT: H 120 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8965 (mm-30) REVERT: H 121 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8205 (mm-30) REVERT: H 124 GLU cc_start: 0.8981 (tp30) cc_final: 0.8719 (tp30) REVERT: H 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9329 (ttt) REVERT: H 127 ARG cc_start: 0.9211 (ttp-110) cc_final: 0.8986 (ttm110) outliers start: 88 outliers final: 55 residues processed: 678 average time/residue: 0.2343 time to fit residues: 237.5380 Evaluate side-chains 693 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 627 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 135 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 114 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: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15228 Z= 0.212 Angle : 0.588 9.976 20644 Z= 0.299 Chirality : 0.038 0.172 2368 Planarity : 0.004 0.061 2576 Dihedral : 3.560 18.293 2104 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.70 % Allowed : 27.56 % Favored : 65.75 % 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: 3.49 (0.20), residues: 1904 helix: 3.09 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 369 HIS 0.005 0.001 HIS D 108 PHE 0.017 0.001 PHE C 260 TYR 0.018 0.001 TYR A 268 ARG 0.011 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 636 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8163 (t60) cc_final: 0.7684 (t60) REVERT: A 180 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7487 (mmt-90) REVERT: A 227 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7743 (ttp80) REVERT: A 499 HIS cc_start: 0.8383 (m-70) cc_final: 0.7956 (p-80) REVERT: A 526 ASP cc_start: 0.9078 (t70) cc_final: 0.8424 (t70) REVERT: A 533 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 9 GLN cc_start: 0.8765 (mp10) cc_final: 0.8312 (pt0) REVERT: B 12 GLU cc_start: 0.9508 (tp30) cc_final: 0.9219 (mm-30) REVERT: B 39 SER cc_start: 0.9372 (t) cc_final: 0.9138 (p) REVERT: B 46 GLU cc_start: 0.9032 (tp30) cc_final: 0.8742 (tp30) REVERT: B 52 MET cc_start: 0.9308 (mtm) cc_final: 0.8931 (mtm) REVERT: B 54 ASN cc_start: 0.8862 (m-40) cc_final: 0.8596 (m110) REVERT: B 72 MET cc_start: 0.9468 (ptm) cc_final: 0.9028 (tmm) REVERT: B 117 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 121 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8094 (mm-30) REVERT: B 124 GLU cc_start: 0.8997 (tp30) cc_final: 0.8725 (tp30) REVERT: B 125 MET cc_start: 0.9616 (ttt) cc_final: 0.9367 (ttp) REVERT: B 127 ARG cc_start: 0.9215 (ttp-110) cc_final: 0.8955 (ttm110) REVERT: C 104 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 166 TRP cc_start: 0.8165 (t60) cc_final: 0.7659 (t60) REVERT: C 180 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7485 (mmt-90) REVERT: C 227 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7731 (ttp80) REVERT: C 499 HIS cc_start: 0.8386 (m-70) cc_final: 0.7959 (p-80) REVERT: C 526 ASP cc_start: 0.9074 (t70) cc_final: 0.8421 (t70) REVERT: C 533 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8429 (tm-30) REVERT: D 9 GLN cc_start: 0.8765 (mp10) cc_final: 0.8313 (pt0) REVERT: D 12 GLU cc_start: 0.9508 (tp30) cc_final: 0.9219 (mm-30) REVERT: D 39 SER cc_start: 0.9344 (t) cc_final: 0.9099 (p) REVERT: D 46 GLU cc_start: 0.9028 (tp30) cc_final: 0.8740 (tp30) REVERT: D 52 MET cc_start: 0.9293 (mtm) cc_final: 0.8868 (mtm) REVERT: D 54 ASN cc_start: 0.8855 (m-40) cc_final: 0.8590 (m110) REVERT: D 72 MET cc_start: 0.9466 (ptm) cc_final: 0.9024 (tmm) REVERT: D 117 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 121 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8091 (mm-30) REVERT: D 124 GLU cc_start: 0.8997 (tp30) cc_final: 0.8726 (tp30) REVERT: D 125 MET cc_start: 0.9617 (ttt) cc_final: 0.9367 (ttp) REVERT: D 127 ARG cc_start: 0.9215 (ttp-110) cc_final: 0.8955 (ttm110) REVERT: E 166 TRP cc_start: 0.8165 (t60) cc_final: 0.7683 (t60) REVERT: E 180 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7489 (mmt-90) REVERT: E 227 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7745 (ttp80) REVERT: E 355 ASN cc_start: 0.8644 (p0) cc_final: 0.8426 (p0) REVERT: E 499 HIS cc_start: 0.8381 (m-70) cc_final: 0.7955 (p-80) REVERT: E 526 ASP cc_start: 0.9077 (t70) cc_final: 0.8425 (t70) REVERT: E 533 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8426 (tm-30) REVERT: F 9 GLN cc_start: 0.8765 (mp10) cc_final: 0.8312 (pt0) REVERT: F 12 GLU cc_start: 0.9508 (tp30) cc_final: 0.9219 (mm-30) REVERT: F 39 SER cc_start: 0.9370 (t) cc_final: 0.9136 (p) REVERT: F 46 GLU cc_start: 0.9032 (tp30) cc_final: 0.8743 (tp30) REVERT: F 52 MET cc_start: 0.9308 (mtm) cc_final: 0.8930 (mtm) REVERT: F 54 ASN cc_start: 0.8857 (m-40) cc_final: 0.8594 (m110) REVERT: F 72 MET cc_start: 0.9467 (ptm) cc_final: 0.9025 (tmm) REVERT: F 117 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8415 (mt) REVERT: F 121 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8094 (mm-30) REVERT: F 124 GLU cc_start: 0.8997 (tp30) cc_final: 0.8725 (tp30) REVERT: F 125 MET cc_start: 0.9616 (ttt) cc_final: 0.9367 (ttp) REVERT: F 127 ARG cc_start: 0.9213 (ttp-110) cc_final: 0.8951 (ttm110) REVERT: G 104 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8653 (tp) REVERT: G 166 TRP cc_start: 0.8166 (t60) cc_final: 0.7659 (t60) REVERT: G 180 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7484 (mmt-90) REVERT: G 227 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7733 (ttp80) REVERT: G 499 HIS cc_start: 0.8382 (m-70) cc_final: 0.7955 (p-80) REVERT: G 526 ASP cc_start: 0.9074 (t70) cc_final: 0.8423 (t70) REVERT: G 533 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 9 GLN cc_start: 0.8767 (mp10) cc_final: 0.8313 (pt0) REVERT: H 12 GLU cc_start: 0.9508 (tp30) cc_final: 0.9219 (mm-30) REVERT: H 39 SER cc_start: 0.9372 (t) cc_final: 0.9137 (p) REVERT: H 46 GLU cc_start: 0.9033 (tp30) cc_final: 0.8744 (tp30) REVERT: H 52 MET cc_start: 0.9308 (mtm) cc_final: 0.8930 (mtm) REVERT: H 54 ASN cc_start: 0.8856 (m-40) cc_final: 0.8595 (m110) REVERT: H 72 MET cc_start: 0.9468 (ptm) cc_final: 0.9025 (tmm) REVERT: H 117 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8412 (mt) REVERT: H 121 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8094 (mm-30) REVERT: H 124 GLU cc_start: 0.8998 (tp30) cc_final: 0.8725 (tp30) REVERT: H 125 MET cc_start: 0.9616 (ttt) cc_final: 0.9367 (ttp) REVERT: H 127 ARG cc_start: 0.9214 (ttp-110) cc_final: 0.8952 (ttm110) outliers start: 97 outliers final: 63 residues processed: 670 average time/residue: 0.2519 time to fit residues: 256.2772 Evaluate side-chains 699 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 626 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 0.0970 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15228 Z= 0.183 Angle : 0.608 10.605 20644 Z= 0.299 Chirality : 0.038 0.168 2368 Planarity : 0.003 0.044 2576 Dihedral : 3.459 17.681 2104 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.70 % Allowed : 29.56 % Favored : 65.75 % 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: 3.44 (0.20), residues: 1904 helix: 3.07 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.78 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 369 HIS 0.006 0.001 HIS B 108 PHE 0.017 0.002 PHE G 260 TYR 0.017 0.001 TYR A 268 ARG 0.010 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 652 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8104 (t60) cc_final: 0.7630 (t60) REVERT: A 180 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7274 (mmt-90) REVERT: A 227 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7783 (ttp80) REVERT: A 499 HIS cc_start: 0.8360 (m-70) cc_final: 0.7926 (p-80) REVERT: A 526 ASP cc_start: 0.8991 (t70) cc_final: 0.8329 (t70) REVERT: A 533 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 534 TYR cc_start: 0.8860 (t80) cc_final: 0.8270 (t80) REVERT: B 9 GLN cc_start: 0.8843 (mp10) cc_final: 0.8371 (pt0) REVERT: B 12 GLU cc_start: 0.9500 (tp30) cc_final: 0.9209 (mm-30) REVERT: B 37 MET cc_start: 0.9196 (mmm) cc_final: 0.8986 (mmm) REVERT: B 39 SER cc_start: 0.9292 (t) cc_final: 0.9055 (p) REVERT: B 52 MET cc_start: 0.9239 (mtm) cc_final: 0.8886 (mtm) REVERT: B 54 ASN cc_start: 0.8810 (m-40) cc_final: 0.8529 (m110) REVERT: B 72 MET cc_start: 0.9461 (ptm) cc_final: 0.9040 (tmm) REVERT: B 117 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 121 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8198 (mm-30) REVERT: B 124 GLU cc_start: 0.9003 (tp30) cc_final: 0.8778 (tp30) REVERT: B 125 MET cc_start: 0.9624 (ttt) cc_final: 0.9340 (ttp) REVERT: B 127 ARG cc_start: 0.9206 (ttp-110) cc_final: 0.8963 (ttm110) REVERT: C 166 TRP cc_start: 0.8163 (t60) cc_final: 0.7655 (t60) REVERT: C 180 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7230 (mtt-85) REVERT: C 227 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7705 (ttp80) REVERT: C 499 HIS cc_start: 0.8361 (m-70) cc_final: 0.7927 (p-80) REVERT: C 526 ASP cc_start: 0.8986 (t70) cc_final: 0.8327 (t70) REVERT: C 533 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 534 TYR cc_start: 0.8858 (t80) cc_final: 0.8286 (t80) REVERT: D 9 GLN cc_start: 0.8842 (mp10) cc_final: 0.8371 (pt0) REVERT: D 12 GLU cc_start: 0.9500 (tp30) cc_final: 0.9210 (mm-30) REVERT: D 39 SER cc_start: 0.9289 (t) cc_final: 0.9050 (p) REVERT: D 52 MET cc_start: 0.9241 (mtm) cc_final: 0.8896 (mtm) REVERT: D 54 ASN cc_start: 0.8816 (m-40) cc_final: 0.8517 (m110) REVERT: D 72 MET cc_start: 0.9458 (ptm) cc_final: 0.9034 (tmm) REVERT: D 117 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8345 (mt) REVERT: D 121 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8195 (mm-30) REVERT: D 124 GLU cc_start: 0.9002 (tp30) cc_final: 0.8778 (tp30) REVERT: D 125 MET cc_start: 0.9623 (ttt) cc_final: 0.9340 (ttp) REVERT: D 127 ARG cc_start: 0.9207 (ttp-110) cc_final: 0.8963 (ttm110) REVERT: E 166 TRP cc_start: 0.8106 (t60) cc_final: 0.7631 (t60) REVERT: E 180 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7274 (mmt-90) REVERT: E 227 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7785 (ttp80) REVERT: E 355 ASN cc_start: 0.8596 (p0) cc_final: 0.8382 (p0) REVERT: E 499 HIS cc_start: 0.8359 (m-70) cc_final: 0.7925 (p-80) REVERT: E 526 ASP cc_start: 0.8989 (t70) cc_final: 0.8330 (t70) REVERT: E 533 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8613 (tm-30) REVERT: E 534 TYR cc_start: 0.8859 (t80) cc_final: 0.8303 (t80) REVERT: F 9 GLN cc_start: 0.8842 (mp10) cc_final: 0.8371 (pt0) REVERT: F 12 GLU cc_start: 0.9499 (tp30) cc_final: 0.9209 (mm-30) REVERT: F 37 MET cc_start: 0.9196 (mmm) cc_final: 0.8985 (mmm) REVERT: F 39 SER cc_start: 0.9293 (t) cc_final: 0.9060 (p) REVERT: F 52 MET cc_start: 0.9242 (mtm) cc_final: 0.8885 (mtm) REVERT: F 54 ASN cc_start: 0.8816 (m-40) cc_final: 0.8478 (m110) REVERT: F 72 MET cc_start: 0.9461 (ptm) cc_final: 0.9038 (tmm) REVERT: F 117 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8344 (mt) REVERT: F 121 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8198 (mm-30) REVERT: F 124 GLU cc_start: 0.9003 (tp30) cc_final: 0.8777 (tp30) REVERT: F 125 MET cc_start: 0.9624 (ttt) cc_final: 0.9340 (ttp) REVERT: F 127 ARG cc_start: 0.9205 (ttp-110) cc_final: 0.8960 (ttm110) REVERT: G 166 TRP cc_start: 0.8144 (t60) cc_final: 0.7630 (t60) REVERT: G 180 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7229 (mtt-85) REVERT: G 227 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7712 (ttp80) REVERT: G 343 LEU cc_start: 0.8921 (mt) cc_final: 0.8579 (mp) REVERT: G 499 HIS cc_start: 0.8360 (m-70) cc_final: 0.7925 (p-80) REVERT: G 526 ASP cc_start: 0.8986 (t70) cc_final: 0.8325 (t70) REVERT: G 533 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8616 (tm-30) REVERT: G 534 TYR cc_start: 0.8862 (t80) cc_final: 0.8285 (t80) REVERT: H 9 GLN cc_start: 0.8843 (mp10) cc_final: 0.8369 (pt0) REVERT: H 12 GLU cc_start: 0.9499 (tp30) cc_final: 0.9209 (mm-30) REVERT: H 37 MET cc_start: 0.9197 (mmm) cc_final: 0.8986 (mmm) REVERT: H 39 SER cc_start: 0.9294 (t) cc_final: 0.9056 (p) REVERT: H 52 MET cc_start: 0.9242 (mtm) cc_final: 0.8886 (mtm) REVERT: H 54 ASN cc_start: 0.8817 (m-40) cc_final: 0.8478 (m110) REVERT: H 72 MET cc_start: 0.9461 (ptm) cc_final: 0.9038 (tmm) REVERT: H 117 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8342 (mt) REVERT: H 121 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8197 (mm-30) REVERT: H 124 GLU cc_start: 0.9002 (tp30) cc_final: 0.8777 (tp30) REVERT: H 125 MET cc_start: 0.9624 (ttt) cc_final: 0.9340 (ttp) REVERT: H 127 ARG cc_start: 0.9207 (ttp-110) cc_final: 0.8960 (ttm110) outliers start: 68 outliers final: 42 residues processed: 675 average time/residue: 0.2231 time to fit residues: 229.5014 Evaluate side-chains 686 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 636 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 163 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15228 Z= 0.437 Angle : 0.704 10.737 20644 Z= 0.370 Chirality : 0.041 0.207 2368 Planarity : 0.005 0.060 2576 Dihedral : 3.777 19.372 2104 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.70 % Allowed : 29.42 % Favored : 63.88 % 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: 3.14 (0.20), residues: 1904 helix: 2.78 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 369 HIS 0.004 0.001 HIS F 108 PHE 0.042 0.003 PHE G 341 TYR 0.023 0.002 TYR E 268 ARG 0.014 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 641 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7562 (mtt-85) REVERT: A 227 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7537 (ttp80) REVERT: A 499 HIS cc_start: 0.8477 (m-70) cc_final: 0.8001 (p-80) REVERT: A 526 ASP cc_start: 0.9143 (t70) cc_final: 0.8571 (t70) REVERT: A 533 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8506 (tm-30) REVERT: B 9 GLN cc_start: 0.8907 (mp10) cc_final: 0.8490 (pt0) REVERT: B 37 MET cc_start: 0.9280 (mmm) cc_final: 0.9065 (mmm) REVERT: B 39 SER cc_start: 0.9394 (t) cc_final: 0.9148 (p) REVERT: B 46 GLU cc_start: 0.9094 (tp30) cc_final: 0.8813 (tp30) REVERT: B 52 MET cc_start: 0.9352 (mtm) cc_final: 0.8938 (mtp) REVERT: B 72 MET cc_start: 0.9463 (ptm) cc_final: 0.9022 (tmm) REVERT: B 121 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8414 (mm-30) REVERT: B 125 MET cc_start: 0.9623 (ttt) cc_final: 0.9262 (ttt) REVERT: C 180 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7519 (mtt-85) REVERT: C 227 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7719 (ttp80) REVERT: C 229 LEU cc_start: 0.9372 (mm) cc_final: 0.9168 (mm) REVERT: C 499 HIS cc_start: 0.8482 (m-70) cc_final: 0.8010 (p-80) REVERT: C 526 ASP cc_start: 0.9143 (t70) cc_final: 0.8571 (t70) REVERT: C 533 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8549 (tm-30) REVERT: C 550 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8807 (mtp-110) REVERT: D 9 GLN cc_start: 0.8907 (mp10) cc_final: 0.8490 (pt0) REVERT: D 39 SER cc_start: 0.9388 (t) cc_final: 0.9146 (p) REVERT: D 52 MET cc_start: 0.9345 (mtm) cc_final: 0.8733 (mtm) REVERT: D 72 MET cc_start: 0.9459 (ptm) cc_final: 0.9015 (tmm) REVERT: D 121 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8412 (mm-30) REVERT: D 125 MET cc_start: 0.9623 (ttt) cc_final: 0.9266 (ttt) REVERT: E 180 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7563 (mtt-85) REVERT: E 227 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7578 (ttp80) REVERT: E 499 HIS cc_start: 0.8475 (m-70) cc_final: 0.7999 (p-80) REVERT: E 526 ASP cc_start: 0.9143 (t70) cc_final: 0.8574 (t70) REVERT: E 533 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8505 (tm-30) REVERT: F 9 GLN cc_start: 0.8907 (mp10) cc_final: 0.8490 (pt0) REVERT: F 37 MET cc_start: 0.9281 (mmm) cc_final: 0.9067 (mmm) REVERT: F 39 SER cc_start: 0.9394 (t) cc_final: 0.9148 (p) REVERT: F 46 GLU cc_start: 0.9103 (tp30) cc_final: 0.8825 (tp30) REVERT: F 52 MET cc_start: 0.9352 (mtm) cc_final: 0.8938 (mtp) REVERT: F 72 MET cc_start: 0.9464 (ptm) cc_final: 0.9020 (tmm) REVERT: F 121 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8414 (mm-30) REVERT: F 125 MET cc_start: 0.9623 (ttt) cc_final: 0.9263 (ttt) REVERT: G 104 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8676 (tp) REVERT: G 180 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7529 (mtt-85) REVERT: G 227 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7728 (ttp80) REVERT: G 229 LEU cc_start: 0.9371 (mm) cc_final: 0.9167 (mm) REVERT: G 499 HIS cc_start: 0.8477 (m-70) cc_final: 0.8001 (p-80) REVERT: G 526 ASP cc_start: 0.9134 (t70) cc_final: 0.8564 (t70) REVERT: G 533 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8535 (tm-30) REVERT: H 9 GLN cc_start: 0.8908 (mp10) cc_final: 0.8490 (pt0) REVERT: H 37 MET cc_start: 0.9281 (mmm) cc_final: 0.9067 (mmm) REVERT: H 39 SER cc_start: 0.9394 (t) cc_final: 0.9148 (p) REVERT: H 46 GLU cc_start: 0.9128 (tp30) cc_final: 0.8856 (tp30) REVERT: H 52 MET cc_start: 0.9352 (mtm) cc_final: 0.8938 (mtp) REVERT: H 72 MET cc_start: 0.9464 (ptm) cc_final: 0.9021 (tmm) REVERT: H 121 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8417 (mm-30) REVERT: H 125 MET cc_start: 0.9623 (ttt) cc_final: 0.9266 (ttt) outliers start: 97 outliers final: 78 residues processed: 669 average time/residue: 0.2312 time to fit residues: 234.3077 Evaluate side-chains 700 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 616 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN D 54 ASN F 54 ASN H 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15228 Z= 0.222 Angle : 0.691 11.982 20644 Z= 0.339 Chirality : 0.040 0.286 2368 Planarity : 0.004 0.063 2576 Dihedral : 3.675 18.703 2104 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.31 % Allowed : 34.05 % Favored : 62.64 % 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: 3.34 (0.20), residues: 1904 helix: 2.85 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 369 HIS 0.002 0.000 HIS E 230 PHE 0.023 0.002 PHE C 341 TYR 0.018 0.002 TYR A 268 ARG 0.014 0.001 ARG D 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 654 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8016 (t60) cc_final: 0.7480 (t60) REVERT: A 180 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7470 (mtt-85) REVERT: A 227 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7453 (ttp80) REVERT: A 499 HIS cc_start: 0.8415 (m-70) cc_final: 0.7932 (p-80) REVERT: A 526 ASP cc_start: 0.9117 (t70) cc_final: 0.8461 (t70) REVERT: A 533 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 9 GLN cc_start: 0.8965 (mp10) cc_final: 0.8537 (pt0) REVERT: B 14 LYS cc_start: 0.8602 (tptp) cc_final: 0.8291 (tppt) REVERT: B 37 MET cc_start: 0.9258 (mmm) cc_final: 0.9041 (mmm) REVERT: B 39 SER cc_start: 0.9306 (t) cc_final: 0.9079 (p) REVERT: B 54 ASN cc_start: 0.8976 (m-40) cc_final: 0.8611 (m110) REVERT: B 72 MET cc_start: 0.9455 (ptm) cc_final: 0.8967 (tmm) REVERT: B 117 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 121 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8328 (mm-30) REVERT: C 104 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8757 (tp) REVERT: C 180 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7476 (mtt-85) REVERT: C 227 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7696 (ttp80) REVERT: C 229 LEU cc_start: 0.9348 (mm) cc_final: 0.9145 (mm) REVERT: C 250 GLN cc_start: 0.8098 (tp40) cc_final: 0.7830 (tp40) REVERT: C 499 HIS cc_start: 0.8425 (m-70) cc_final: 0.7946 (p-80) REVERT: C 509 MET cc_start: 0.9392 (mtp) cc_final: 0.9126 (ttm) REVERT: C 526 ASP cc_start: 0.9114 (t70) cc_final: 0.8462 (t70) REVERT: C 533 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 534 TYR cc_start: 0.8962 (t80) cc_final: 0.8717 (t80) REVERT: C 550 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8867 (mtp-110) REVERT: D 9 GLN cc_start: 0.8965 (mp10) cc_final: 0.8537 (pt0) REVERT: D 14 LYS cc_start: 0.8603 (tptp) cc_final: 0.8293 (tppt) REVERT: D 39 SER cc_start: 0.9433 (t) cc_final: 0.9195 (p) REVERT: D 52 MET cc_start: 0.9304 (mtm) cc_final: 0.8877 (mtm) REVERT: D 54 ASN cc_start: 0.8964 (m-40) cc_final: 0.8583 (m-40) REVERT: D 72 MET cc_start: 0.9453 (ptm) cc_final: 0.8925 (tmm) REVERT: D 117 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8521 (mt) REVERT: D 121 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8328 (mm-30) REVERT: E 166 TRP cc_start: 0.8016 (t60) cc_final: 0.7480 (t60) REVERT: E 180 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7472 (mtt-85) REVERT: E 227 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7454 (ttp80) REVERT: E 251 GLU cc_start: 0.9124 (tp30) cc_final: 0.8904 (tp30) REVERT: E 499 HIS cc_start: 0.8413 (m-70) cc_final: 0.7931 (p-80) REVERT: E 526 ASP cc_start: 0.9112 (t70) cc_final: 0.8458 (t70) REVERT: E 533 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8634 (tm-30) REVERT: F 9 GLN cc_start: 0.8966 (mp10) cc_final: 0.8538 (pt0) REVERT: F 14 LYS cc_start: 0.8602 (tptp) cc_final: 0.8292 (tppt) REVERT: F 37 MET cc_start: 0.9261 (mmm) cc_final: 0.9043 (mmm) REVERT: F 39 SER cc_start: 0.9305 (t) cc_final: 0.9079 (p) REVERT: F 54 ASN cc_start: 0.8942 (m-40) cc_final: 0.8543 (m-40) REVERT: F 72 MET cc_start: 0.9457 (ptm) cc_final: 0.8966 (tmm) REVERT: F 117 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8520 (mt) REVERT: F 121 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8328 (mm-30) REVERT: G 180 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7471 (mtt-85) REVERT: G 227 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7685 (ttp80) REVERT: G 229 LEU cc_start: 0.9347 (mm) cc_final: 0.9144 (mm) REVERT: G 250 GLN cc_start: 0.8097 (tp40) cc_final: 0.7831 (tp40) REVERT: G 499 HIS cc_start: 0.8415 (m-70) cc_final: 0.7932 (p-80) REVERT: G 526 ASP cc_start: 0.9088 (t70) cc_final: 0.8398 (t70) REVERT: G 533 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8404 (tm-30) REVERT: H 9 GLN cc_start: 0.8965 (mp10) cc_final: 0.8536 (pt0) REVERT: H 14 LYS cc_start: 0.8601 (tptp) cc_final: 0.8291 (tppt) REVERT: H 37 MET cc_start: 0.9260 (mmm) cc_final: 0.9042 (mmm) REVERT: H 39 SER cc_start: 0.9305 (t) cc_final: 0.9079 (p) REVERT: H 46 GLU cc_start: 0.9076 (tp30) cc_final: 0.8814 (tp30) REVERT: H 54 ASN cc_start: 0.8942 (m-40) cc_final: 0.8542 (m-40) REVERT: H 72 MET cc_start: 0.9457 (ptm) cc_final: 0.8967 (tmm) REVERT: H 117 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8523 (mt) REVERT: H 121 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8330 (mm-30) outliers start: 48 outliers final: 34 residues processed: 672 average time/residue: 0.2521 time to fit residues: 253.3434 Evaluate side-chains 660 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 616 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 156 optimal weight: 0.0040 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077242 restraints weight = 38089.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080121 restraints weight = 19365.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082148 restraints weight = 12269.615| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15228 Z= 0.206 Angle : 0.677 12.422 20644 Z= 0.329 Chirality : 0.038 0.211 2368 Planarity : 0.004 0.060 2576 Dihedral : 3.514 18.137 2104 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.49 % Allowed : 36.33 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.20), residues: 1904 helix: 2.77 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 369 HIS 0.004 0.000 HIS H 108 PHE 0.022 0.001 PHE G 341 TYR 0.017 0.001 TYR C 268 ARG 0.014 0.001 ARG D 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4275.21 seconds wall clock time: 77 minutes 7.51 seconds (4627.51 seconds total)