Starting phenix.real_space_refine on Sun Mar 17 10:22:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/03_2024/6vxk_21442.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/03_2024/6vxk_21442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/03_2024/6vxk_21442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/03_2024/6vxk_21442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/03_2024/6vxk_21442.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/03_2024/6vxk_21442.pdb" } resolution = 3.1 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 10988 2.51 5 N 2960 2.21 5 O 3372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B ASP 704": "OD1" <-> "OD2" Residue "B PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D ARG 320": "NH1" <-> "NH2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D ASP 704": "OD1" <-> "OD2" Residue "D PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 830": "OD1" <-> "OD2" Residue "D TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3022 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 361} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5561 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 714} Chain breaks: 12 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3022 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 361} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5561 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 714} Chain breaks: 12 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.99, per 1000 atoms: 0.52 Number of scatterers: 17418 At special positions: 0 Unit cell: (202.86, 101.844, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3372 8.00 N 2960 7.00 C 10988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 286 " distance=2.02 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 703 " distance=2.04 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 506 " distance=2.02 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 835 " distance=2.03 Simple disulfide: pdb=" SG CYS B 801 " - pdb=" SG CYS B 806 " distance=2.04 Simple disulfide: pdb=" SG CYS B 891 " - pdb=" SG CYS B 907 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 286 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 226 " - pdb=" SG CYS D 354 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 412 " - pdb=" SG CYS D 703 " distance=2.04 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 461 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 464 " - pdb=" SG CYS D 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 475 " - pdb=" SG CYS D 487 " distance=2.03 Simple disulfide: pdb=" SG CYS D 734 " - pdb=" SG CYS D 742 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 835 " distance=2.03 Simple disulfide: pdb=" SG CYS D 801 " - pdb=" SG CYS D 806 " distance=2.04 Simple disulfide: pdb=" SG CYS D 891 " - pdb=" SG CYS D 907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 53 " " NAG B1601 " - " ASN B 141 " " NAG B1602 " - " ASN B 241 " " NAG B1603 " - " ASN B 149 " " NAG B1604 " - " ASN B 252 " " NAG B1605 " - " ASN B 86 " " NAG B1606 " - " ASN B 715 " " NAG B1607 " - " ASN B 771 " " NAG B1608 " - " ASN B 871 " " NAG C 501 " - " ASN C 53 " " NAG D1601 " - " ASN D 141 " " NAG D1602 " - " ASN D 241 " " NAG D1603 " - " ASN D 149 " " NAG D1604 " - " ASN D 252 " " NAG D1605 " - " ASN D 86 " " NAG D1606 " - " ASN D 715 " " NAG D1607 " - " ASN D 771 " " NAG D1608 " - " ASN D 871 " Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 3.1 seconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 50 sheets defined 5.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.715A pdb=" N SER A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.547A pdb=" N CYS B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.747A pdb=" N CYS B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.716A pdb=" N SER C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 205 " --> pdb=" O LEU C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 205' Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.547A pdb=" N CYS D 464 " --> pdb=" O SER D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 494 No H-bonds generated for 'chain 'D' and resid 492 through 494' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.747A pdb=" N CYS D 506 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.365A pdb=" N ILE A 64 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 78 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 162 removed outlier: 7.148A pdb=" N LYS A 212 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP A 309 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU A 214 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.356A pdb=" N CYS A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 234 removed outlier: 6.765A pdb=" N PHE A 244 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A 230 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 242 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 232 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A 240 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.857A pdb=" N VAL B 430 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.605A pdb=" N SER B 77 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 112 Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 169 removed outlier: 4.957A pdb=" N ALA B 204 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY B 221 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N ASP B 209 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N GLU B 219 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AB5, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.290A pdb=" N ALA B 268 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 275 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 363 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER B 280 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 293 through 300 removed outlier: 6.511A pdb=" N VAL B 309 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 297 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 307 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU B 299 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 305 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 383 removed outlier: 6.435A pdb=" N LYS B 401 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL B 415 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB9, first strand: chain 'B' and resid 508 through 510 Processing sheet with id=AC1, first strand: chain 'B' and resid 546 through 548 Processing sheet with id=AC2, first strand: chain 'B' and resid 663 through 668 removed outlier: 3.729A pdb=" N TYR B 663 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 683 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 667 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 681 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE B 721 " --> pdb=" O ASN B 679 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 681 " --> pdb=" O MET B 719 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET B 719 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 671 through 673 removed outlier: 6.909A pdb=" N VAL B 672 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 744 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 735 " --> pdb=" O SER B 744 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 746 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 756 through 759 removed outlier: 3.630A pdb=" N GLY B 807 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 763 through 765 removed outlier: 5.140A pdb=" N TYR B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 828 " --> pdb=" O TYR B 832 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP B 834 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU B 826 " --> pdb=" O ASP B 834 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY B 836 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL B 824 " --> pdb=" O GLY B 836 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 846 through 849 Processing sheet with id=AC7, first strand: chain 'B' and resid 877 through 880 Processing sheet with id=AC8, first strand: chain 'C' and resid 14 through 19 Processing sheet with id=AC9, first strand: chain 'C' and resid 26 through 32 Processing sheet with id=AD1, first strand: chain 'C' and resid 63 through 66 removed outlier: 6.365A pdb=" N ILE C 64 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 78 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AD3, first strand: chain 'C' and resid 157 through 162 removed outlier: 7.148A pdb=" N LYS C 212 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP C 309 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 214 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 217 through 218 removed outlier: 4.357A pdb=" N CYS C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 226 through 234 removed outlier: 6.766A pdb=" N PHE C 244 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 230 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR C 242 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 232 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 240 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 332 Processing sheet with id=AD7, first strand: chain 'D' and resid 39 through 41 removed outlier: 3.857A pdb=" N VAL D 430 " --> pdb=" O TYR D 440 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.605A pdb=" N SER D 77 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 108 through 112 Processing sheet with id=AE1, first strand: chain 'D' and resid 162 through 169 removed outlier: 4.957A pdb=" N ALA D 204 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY D 221 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N ASP D 209 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N GLU D 219 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 231 through 234 Processing sheet with id=AE3, first strand: chain 'D' and resid 231 through 234 removed outlier: 6.290A pdb=" N ALA D 268 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE D 275 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL D 363 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER D 280 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 293 through 300 removed outlier: 6.512A pdb=" N VAL D 309 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 297 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA D 307 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU D 299 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 305 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 378 through 383 removed outlier: 6.435A pdb=" N LYS D 401 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL D 415 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 480 through 482 Processing sheet with id=AE7, first strand: chain 'D' and resid 508 through 510 Processing sheet with id=AE8, first strand: chain 'D' and resid 546 through 548 Processing sheet with id=AE9, first strand: chain 'D' and resid 663 through 668 removed outlier: 3.729A pdb=" N TYR D 663 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 683 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE D 667 " --> pdb=" O ILE D 681 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 681 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE D 721 " --> pdb=" O ASN D 679 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 681 " --> pdb=" O MET D 719 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET D 719 " --> pdb=" O ILE D 681 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 671 through 673 removed outlier: 6.909A pdb=" N VAL D 672 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER D 744 " --> pdb=" O ILE D 735 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 735 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 746 " --> pdb=" O VAL D 733 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 756 through 759 removed outlier: 3.630A pdb=" N GLY D 807 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 763 through 765 removed outlier: 5.140A pdb=" N TYR D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL D 828 " --> pdb=" O TYR D 832 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP D 834 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU D 826 " --> pdb=" O ASP D 834 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY D 836 " --> pdb=" O VAL D 824 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 824 " --> pdb=" O GLY D 836 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 846 through 849 Processing sheet with id=AF5, first strand: chain 'D' and resid 877 through 880 568 hydrogen bonds defined for protein. 1440 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: 7.01 Time building geometry restraints manager: 6.59 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: 5558 1.33 - 1.45: 3598 1.45 - 1.58: 8484 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 17764 Sorted by residual: bond pdb=" C ILE A 311 " pdb=" N LYS A 312 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.81e+01 bond pdb=" C ILE C 311 " pdb=" N LYS C 312 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.79e+01 bond pdb=" CA ARG C 368 " pdb=" CB ARG C 368 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.76e-02 3.23e+03 6.73e+00 bond pdb=" CA ARG A 368 " pdb=" CB ARG A 368 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.76e-02 3.23e+03 6.62e+00 bond pdb=" CA SER C 252 " pdb=" CB SER C 252 " ideal model delta sigma weight residual 1.536 1.488 0.047 2.08e-02 2.31e+03 5.18e+00 ... (remaining 17759 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.46: 462 106.46 - 113.34: 10237 113.34 - 120.22: 5770 120.22 - 127.09: 7441 127.09 - 133.97: 200 Bond angle restraints: 24110 Sorted by residual: angle pdb=" C ASN B 411 " pdb=" N CYS B 412 " pdb=" CA CYS B 412 " ideal model delta sigma weight residual 120.67 112.83 7.84 1.34e+00 5.57e-01 3.43e+01 angle pdb=" C ASN D 411 " pdb=" N CYS D 412 " pdb=" CA CYS D 412 " ideal model delta sigma weight residual 120.67 112.83 7.84 1.34e+00 5.57e-01 3.43e+01 angle pdb=" CA CYS D 806 " pdb=" CB CYS D 806 " pdb=" SG CYS D 806 " ideal model delta sigma weight residual 114.40 126.17 -11.77 2.30e+00 1.89e-01 2.62e+01 angle pdb=" CA CYS B 806 " pdb=" CB CYS B 806 " pdb=" SG CYS B 806 " ideal model delta sigma weight residual 114.40 126.13 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" N CYS D 801 " pdb=" CA CYS D 801 " pdb=" C CYS D 801 " ideal model delta sigma weight residual 109.52 117.32 -7.80 1.55e+00 4.16e-01 2.53e+01 ... (remaining 24105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9612 17.70 - 35.39: 1032 35.39 - 53.09: 216 53.09 - 70.79: 46 70.79 - 88.49: 16 Dihedral angle restraints: 10922 sinusoidal: 4430 harmonic: 6492 Sorted by residual: dihedral pdb=" CB CYS D 801 " pdb=" SG CYS D 801 " pdb=" SG CYS D 806 " pdb=" CB CYS D 806 " ideal model delta sinusoidal sigma weight residual 93.00 4.51 88.49 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS B 801 " pdb=" SG CYS B 801 " pdb=" SG CYS B 806 " pdb=" CB CYS B 806 " ideal model delta sinusoidal sigma weight residual 93.00 4.53 88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS B 156 " pdb=" SG CYS B 156 " pdb=" SG CYS B 194 " pdb=" CB CYS B 194 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 10919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2372 0.076 - 0.152: 411 0.152 - 0.228: 11 0.228 - 0.304: 4 0.304 - 0.380: 2 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG D1608 " pdb=" ND2 ASN D 871 " pdb=" C2 NAG D1608 " pdb=" O5 NAG D1608 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1608 " pdb=" ND2 ASN B 871 " pdb=" C2 NAG B1608 " pdb=" O5 NAG B1608 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1603 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1603 " pdb=" O5 NAG B1603 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2797 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 246 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO D 247 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 247 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 247 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 247 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 322 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 323 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 323 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 323 " -0.024 5.00e-02 4.00e+02 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 814 2.68 - 3.23: 16847 3.23 - 3.79: 27515 3.79 - 4.34: 36152 4.34 - 4.90: 62003 Nonbonded interactions: 143331 Sorted by model distance: nonbonded pdb=" O TRP B 175 " pdb=" OG1 THR B 210 " model vdw 2.122 2.440 nonbonded pdb=" O TRP D 175 " pdb=" OG1 THR D 210 " model vdw 2.122 2.440 nonbonded pdb=" O THR A 73 " pdb=" OG1 THR A 73 " model vdw 2.139 2.440 nonbonded pdb=" O THR C 73 " pdb=" OG1 THR C 73 " model vdw 2.139 2.440 nonbonded pdb=" OE2 GLU A 24 " pdb=" OH TYR A 45 " model vdw 2.160 2.440 ... (remaining 143326 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' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.540 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 46.440 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.011 0.088 17764 Z= 0.749 Angle : 0.841 11.770 24110 Z= 0.463 Chirality : 0.053 0.380 2800 Planarity : 0.004 0.047 3068 Dihedral : 14.805 87.569 6640 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 8.05 % Allowed : 17.01 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -3.69 (0.15), residues: 2198 helix: -2.73 (0.43), residues: 96 sheet: -1.59 (0.17), residues: 762 loop : -3.11 (0.13), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 765 HIS 0.006 0.001 HIS C 337 PHE 0.020 0.002 PHE C 344 TYR 0.016 0.002 TYR A 351 ARG 0.005 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 69 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 GLN cc_start: 0.7858 (pt0) cc_final: 0.7623 (pp30) REVERT: B 113 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: B 730 MET cc_start: 0.8480 (ttm) cc_final: 0.8057 (ttm) REVERT: B 760 PHE cc_start: 0.7387 (m-80) cc_final: 0.7078 (t80) REVERT: D 113 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7954 (ttm-80) REVERT: D 730 MET cc_start: 0.8484 (ttm) cc_final: 0.8060 (ttm) REVERT: D 760 PHE cc_start: 0.7394 (m-80) cc_final: 0.7080 (t80) outliers start: 149 outliers final: 95 residues processed: 208 average time/residue: 0.2623 time to fit residues: 89.5145 Evaluate side-chains 153 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 56 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 264 HIS A 295 HIS B 67 GLN B 218 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 HIS B 670 GLN B 709 GLN B 718 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 829 GLN C 80 ASN C 264 HIS C 295 HIS C 348 ASN D 67 GLN D 218 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 HIS D 670 GLN D 709 GLN D 718 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN D 829 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17764 Z= 0.196 Angle : 0.598 9.888 24110 Z= 0.306 Chirality : 0.047 0.320 2800 Planarity : 0.004 0.037 3068 Dihedral : 8.847 69.547 2934 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.94 % Allowed : 21.49 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.80 (0.16), residues: 2198 helix: -1.74 (0.52), residues: 110 sheet: -1.05 (0.18), residues: 760 loop : -2.47 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.001 0.000 HIS D 718 PHE 0.016 0.001 PHE A 344 TYR 0.012 0.001 TYR C 351 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 61 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8636 (pm20) cc_final: 0.8400 (pm20) REVERT: A 316 GLN cc_start: 0.8241 (pp30) cc_final: 0.8031 (pp30) REVERT: A 337 HIS cc_start: 0.7361 (m-70) cc_final: 0.7128 (m-70) REVERT: B 137 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8189 (ptp-110) REVERT: B 523 MET cc_start: 0.7492 (mmp) cc_final: 0.7182 (mmp) REVERT: B 760 PHE cc_start: 0.7293 (m-80) cc_final: 0.6992 (t80) REVERT: B 800 TYR cc_start: 0.6108 (t80) cc_final: 0.5899 (t80) REVERT: C 105 GLN cc_start: 0.8559 (pm20) cc_final: 0.8245 (pm20) REVERT: C 337 HIS cc_start: 0.7763 (m-70) cc_final: 0.7528 (m-70) REVERT: D 137 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8189 (ptp-110) REVERT: D 523 MET cc_start: 0.7493 (mmp) cc_final: 0.7182 (mmp) REVERT: D 760 PHE cc_start: 0.7299 (m-80) cc_final: 0.6996 (t80) REVERT: D 800 TYR cc_start: 0.6099 (t80) cc_final: 0.5892 (t80) outliers start: 73 outliers final: 46 residues processed: 127 average time/residue: 0.2908 time to fit residues: 57.2231 Evaluate side-chains 104 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 56 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 50.0000 chunk 181 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 GLN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17764 Z= 0.315 Angle : 0.615 11.033 24110 Z= 0.314 Chirality : 0.047 0.324 2800 Planarity : 0.004 0.039 3068 Dihedral : 7.356 59.644 2842 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.67 % Allowed : 20.52 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.45 (0.17), residues: 2198 helix: -1.10 (0.58), residues: 98 sheet: -0.97 (0.18), residues: 798 loop : -2.17 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 345 HIS 0.002 0.001 HIS D 157 PHE 0.019 0.001 PHE A 344 TYR 0.014 0.001 TYR C 351 ARG 0.009 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 57 time to evaluate : 2.118 Fit side-chains REVERT: A 244 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7871 (t80) REVERT: A 316 GLN cc_start: 0.8239 (pp30) cc_final: 0.8025 (pp30) REVERT: A 337 HIS cc_start: 0.7301 (m-70) cc_final: 0.7054 (m-70) REVERT: A 359 GLN cc_start: 0.7760 (pp30) cc_final: 0.7514 (pp30) REVERT: B 137 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8375 (ptp-110) REVERT: B 760 PHE cc_start: 0.7297 (m-80) cc_final: 0.6998 (t80) REVERT: B 907 CYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5918 (m) REVERT: C 105 GLN cc_start: 0.8571 (pm20) cc_final: 0.8280 (pm20) REVERT: C 244 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7920 (t80) REVERT: D 137 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8373 (ptp-110) REVERT: D 760 PHE cc_start: 0.7305 (m-80) cc_final: 0.6999 (t80) REVERT: D 907 CYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5908 (m) outliers start: 105 outliers final: 67 residues processed: 153 average time/residue: 0.2783 time to fit residues: 67.7444 Evaluate side-chains 128 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 55 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17764 Z= 0.414 Angle : 0.656 12.675 24110 Z= 0.334 Chirality : 0.048 0.328 2800 Planarity : 0.004 0.036 3068 Dihedral : 7.197 57.555 2826 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.78 % Allowed : 20.68 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.35 (0.17), residues: 2198 helix: -1.49 (0.53), residues: 110 sheet: -0.84 (0.18), residues: 784 loop : -2.10 (0.15), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 207 HIS 0.005 0.001 HIS D 157 PHE 0.020 0.002 PHE C 344 TYR 0.016 0.002 TYR D 663 ARG 0.008 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 57 time to evaluate : 1.858 Fit side-chains REVERT: A 244 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7882 (t80) REVERT: A 316 GLN cc_start: 0.8271 (pp30) cc_final: 0.8025 (pp30) REVERT: A 337 HIS cc_start: 0.7297 (m-70) cc_final: 0.7065 (m-70) REVERT: B 113 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7982 (ttm-80) REVERT: B 137 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8299 (ptp-110) REVERT: B 760 PHE cc_start: 0.7279 (m-80) cc_final: 0.6976 (t80) REVERT: B 907 CYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5972 (m) REVERT: C 219 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 244 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7888 (t80) REVERT: C 359 GLN cc_start: 0.7731 (pp30) cc_final: 0.7402 (pp30) REVERT: D 113 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7986 (ttm-80) REVERT: D 137 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8296 (ptp-110) REVERT: D 760 PHE cc_start: 0.7284 (m-80) cc_final: 0.6976 (t80) REVERT: D 907 CYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5957 (m) outliers start: 107 outliers final: 84 residues processed: 155 average time/residue: 0.2598 time to fit residues: 63.7659 Evaluate side-chains 149 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 56 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17764 Z= 0.373 Angle : 0.629 11.167 24110 Z= 0.321 Chirality : 0.047 0.328 2800 Planarity : 0.004 0.036 3068 Dihedral : 7.021 58.130 2826 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 6.32 % Allowed : 20.84 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.23 (0.17), residues: 2198 helix: -1.44 (0.53), residues: 110 sheet: -0.78 (0.18), residues: 788 loop : -2.00 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.003 0.001 HIS D 157 PHE 0.019 0.002 PHE C 344 TYR 0.014 0.001 TYR C 351 ARG 0.008 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 59 time to evaluate : 1.918 Fit side-chains REVERT: A 244 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7882 (t80) REVERT: A 316 GLN cc_start: 0.8273 (pp30) cc_final: 0.7993 (pp30) REVERT: A 337 HIS cc_start: 0.7314 (m-70) cc_final: 0.7042 (m-70) REVERT: A 338 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7638 (tpp80) REVERT: A 358 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8321 (mttt) REVERT: A 359 GLN cc_start: 0.7865 (pp30) cc_final: 0.7640 (pp30) REVERT: B 113 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7948 (ttm-80) REVERT: B 137 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8390 (ptp-110) REVERT: B 760 PHE cc_start: 0.7264 (m-80) cc_final: 0.6969 (t80) REVERT: B 907 CYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5983 (m) REVERT: C 219 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8832 (mm) REVERT: C 244 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7881 (t80) REVERT: C 359 GLN cc_start: 0.7776 (pp30) cc_final: 0.7463 (pp30) REVERT: D 113 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7968 (ttm-80) REVERT: D 137 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8388 (ptp-110) REVERT: D 351 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6996 (pp20) REVERT: D 760 PHE cc_start: 0.7272 (m-80) cc_final: 0.6971 (t80) REVERT: D 907 CYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5965 (m) outliers start: 117 outliers final: 96 residues processed: 167 average time/residue: 0.2684 time to fit residues: 71.5862 Evaluate side-chains 164 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 57 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.6980 chunk 194 optimal weight: 0.0870 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17764 Z= 0.144 Angle : 0.552 11.254 24110 Z= 0.281 Chirality : 0.046 0.319 2800 Planarity : 0.003 0.037 3068 Dihedral : 6.300 55.015 2826 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.32 % Allowed : 22.79 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2198 helix: -1.16 (0.54), residues: 110 sheet: -0.59 (0.19), residues: 774 loop : -1.80 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 86 HIS 0.001 0.000 HIS C 337 PHE 0.012 0.001 PHE C 344 TYR 0.016 0.001 TYR D 663 ARG 0.005 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 66 time to evaluate : 2.049 Fit side-chains REVERT: A 79 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8629 (p0) REVERT: A 105 GLN cc_start: 0.8614 (pm20) cc_final: 0.8390 (pm20) REVERT: A 244 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7805 (t80) REVERT: A 337 HIS cc_start: 0.7233 (m-70) cc_final: 0.7013 (m-70) REVERT: A 338 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7594 (tpp80) REVERT: B 113 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: C 105 GLN cc_start: 0.8567 (pm20) cc_final: 0.8090 (pm20) REVERT: C 244 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7815 (t80) REVERT: C 359 GLN cc_start: 0.7687 (pp30) cc_final: 0.7472 (pp30) REVERT: D 113 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: D 760 PHE cc_start: 0.7194 (m-80) cc_final: 0.6994 (t80) outliers start: 80 outliers final: 59 residues processed: 140 average time/residue: 0.2607 time to fit residues: 58.9049 Evaluate side-chains 126 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 62 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.0770 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 121 optimal weight: 0.0570 chunk 215 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 99 optimal weight: 0.0270 overall best weight: 1.0316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17764 Z= 0.180 Angle : 0.549 10.568 24110 Z= 0.280 Chirality : 0.046 0.400 2800 Planarity : 0.003 0.036 3068 Dihedral : 6.140 56.210 2820 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.08 % Allowed : 22.25 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2198 helix: -1.02 (0.55), residues: 110 sheet: -0.49 (0.19), residues: 778 loop : -1.70 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 327 HIS 0.001 0.000 HIS D 755 PHE 0.013 0.001 PHE C 344 TYR 0.011 0.001 TYR C 351 ARG 0.004 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 63 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8600 (pm20) cc_final: 0.8354 (pm20) REVERT: A 244 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7799 (t80) REVERT: A 316 GLN cc_start: 0.8119 (pp30) cc_final: 0.7918 (pp30) REVERT: A 337 HIS cc_start: 0.7223 (m-70) cc_final: 0.6995 (m-70) REVERT: A 338 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7642 (tpp80) REVERT: B 113 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7943 (ttm-80) REVERT: B 137 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8081 (ptp-110) REVERT: B 351 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: B 907 CYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5771 (m) REVERT: C 244 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7869 (t80) REVERT: C 359 GLN cc_start: 0.7644 (pp30) cc_final: 0.7417 (pp30) REVERT: D 113 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7948 (ttm-80) REVERT: D 137 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8055 (ptp-110) REVERT: D 760 PHE cc_start: 0.7174 (m-80) cc_final: 0.6966 (t80) REVERT: D 907 CYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5773 (m) outliers start: 94 outliers final: 66 residues processed: 151 average time/residue: 0.2870 time to fit residues: 67.2684 Evaluate side-chains 136 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 61 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17764 Z= 0.329 Angle : 0.587 9.497 24110 Z= 0.301 Chirality : 0.047 0.352 2800 Planarity : 0.004 0.035 3068 Dihedral : 6.323 59.481 2816 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.72 % Allowed : 21.98 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2198 helix: -1.00 (0.54), residues: 110 sheet: -0.45 (0.19), residues: 784 loop : -1.71 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.001 HIS B 157 PHE 0.024 0.002 PHE B 760 TYR 0.017 0.001 TYR B 663 ARG 0.006 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 55 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 316 GLN cc_start: 0.8176 (pp30) cc_final: 0.7939 (pp30) REVERT: A 338 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7675 (tpp80) REVERT: B 113 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: B 137 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8037 (ptp-110) REVERT: B 351 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6987 (pp20) REVERT: B 907 CYS cc_start: 0.6045 (OUTLIER) cc_final: 0.5797 (m) REVERT: C 219 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8794 (mm) REVERT: C 244 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 335 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8152 (p0) REVERT: C 359 GLN cc_start: 0.7689 (pp30) cc_final: 0.7403 (pp30) REVERT: D 113 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7946 (ttm-80) REVERT: D 137 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8012 (ptp-110) REVERT: D 351 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6967 (pp20) REVERT: D 760 PHE cc_start: 0.7225 (m-80) cc_final: 0.6987 (t80) REVERT: D 907 CYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5816 (m) outliers start: 106 outliers final: 81 residues processed: 154 average time/residue: 0.2567 time to fit residues: 64.0260 Evaluate side-chains 147 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 54 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17764 Z= 0.375 Angle : 0.611 9.499 24110 Z= 0.313 Chirality : 0.047 0.345 2800 Planarity : 0.004 0.034 3068 Dihedral : 6.540 57.674 2816 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.56 % Allowed : 22.03 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 2198 helix: -1.04 (0.54), residues: 110 sheet: -0.49 (0.18), residues: 784 loop : -1.73 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 327 HIS 0.003 0.001 HIS B 157 PHE 0.020 0.002 PHE A 344 TYR 0.015 0.001 TYR A 351 ARG 0.004 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 54 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7892 (t80) REVERT: A 316 GLN cc_start: 0.8223 (pp30) cc_final: 0.7969 (pp30) REVERT: A 338 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7719 (tpp80) REVERT: B 113 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: B 351 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6986 (pp20) REVERT: B 907 CYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5816 (m) REVERT: C 219 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8784 (mm) REVERT: C 244 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7883 (t80) REVERT: C 337 HIS cc_start: 0.7448 (m-70) cc_final: 0.7238 (m-70) REVERT: C 359 GLN cc_start: 0.7679 (pp30) cc_final: 0.7397 (pp30) REVERT: D 113 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7950 (ttm-80) REVERT: D 351 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: D 760 PHE cc_start: 0.7253 (m-80) cc_final: 0.6943 (t80) REVERT: D 907 CYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5819 (m) outliers start: 103 outliers final: 85 residues processed: 152 average time/residue: 0.2668 time to fit residues: 64.7633 Evaluate side-chains 148 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 54 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 50.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17764 Z= 0.188 Angle : 0.552 9.589 24110 Z= 0.282 Chirality : 0.046 0.331 2800 Planarity : 0.003 0.035 3068 Dihedral : 6.163 57.801 2816 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.37 % Allowed : 23.76 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2198 helix: -0.87 (0.55), residues: 110 sheet: -0.36 (0.19), residues: 760 loop : -1.65 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.000 HIS D 755 PHE 0.014 0.001 PHE A 344 TYR 0.018 0.001 TYR D 663 ARG 0.005 0.000 ARG C 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 57 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7811 (t80) REVERT: A 316 GLN cc_start: 0.8136 (pp30) cc_final: 0.7888 (pp30) REVERT: B 113 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7933 (ttm-80) REVERT: B 351 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6972 (pp20) REVERT: B 907 CYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5846 (m) REVERT: C 219 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8751 (mm) REVERT: C 244 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7805 (t80) REVERT: C 359 GLN cc_start: 0.7657 (pp30) cc_final: 0.7428 (pp30) REVERT: D 113 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7936 (ttm-80) REVERT: D 760 PHE cc_start: 0.7199 (m-80) cc_final: 0.6939 (t80) REVERT: D 907 CYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5829 (m) outliers start: 81 outliers final: 67 residues processed: 134 average time/residue: 0.2578 time to fit residues: 56.8933 Evaluate side-chains 130 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 55 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 907 CYS Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.0270 chunk 189 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.079639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054235 restraints weight = 54526.212| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.31 r_work: 0.2906 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17764 Z= 0.153 Angle : 0.531 9.589 24110 Z= 0.270 Chirality : 0.045 0.328 2800 Planarity : 0.003 0.036 3068 Dihedral : 5.646 55.169 2812 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.00 % Allowed : 24.08 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2198 helix: -0.79 (0.56), residues: 110 sheet: -0.22 (0.19), residues: 772 loop : -1.63 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 86 HIS 0.002 0.000 HIS D 755 PHE 0.012 0.001 PHE A 344 TYR 0.010 0.001 TYR A 351 ARG 0.005 0.000 ARG C 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.48 seconds wall clock time: 60 minutes 55.44 seconds (3655.44 seconds total)