Starting phenix.real_space_refine on Fri Feb 23 01:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5j_31725/02_2024/7v5j_31725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5j_31725/02_2024/7v5j_31725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5j_31725/02_2024/7v5j_31725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5j_31725/02_2024/7v5j_31725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5j_31725/02_2024/7v5j_31725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5j_31725/02_2024/7v5j_31725.pdb" } resolution = 2.8 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 191 5.16 5 C 22950 2.51 5 N 5975 2.21 5 O 7073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 664": "OD1" <-> "OD2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1090": "OE1" <-> "OE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1195": "OE1" <-> "OE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 664": "OD1" <-> "OD2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 818": "OE1" <-> "OE2" Residue "C GLU 875": "OE1" <-> "OE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1062": "OE1" <-> "OE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36189 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8770 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 50, 'TRANS': 1082} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8796 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 50, 'TRANS': 1086} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 8794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1135, 8788 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1085} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 1135, 8788 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1085} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 8979 Chain: "D" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1591 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "F" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "I" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 21.01, per 1000 atoms: 0.58 Number of scatterers: 36189 At special positions: 0 Unit cell: (218.665, 231.655, 167.787, 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 191 16.00 O 7073 8.00 N 5975 7.00 C 22950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.05 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.05 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.04 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.04 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 151 " - pdb=" SG CYS I 207 " 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 Time building additional restraints: 13.10 Conformation dependent library (CDL) restraints added in 8.2 seconds 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8750 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 84 sheets defined 18.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.604A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.995A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.808A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.926A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.936A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.788A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 940 through 960 removed outlier: 4.528A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 987 through 994 Processing helix chain 'A' and resid 996 through 1011 Processing helix chain 'A' and resid 1016 through 1037 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.663A pdb=" N ARG A1069 " --> pdb=" O ALA A1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 221 through 232 removed outlier: 4.224A pdb=" N LEU B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 410 through 418 removed outlier: 4.254A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.281A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 4.109A pdb=" N GLN B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.846A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 824 through 854 Processing helix chain 'B' and resid 862 through 866 removed outlier: 4.245A pdb=" N GLY B 866 " --> pdb=" O PRO B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 940 through 960 removed outlier: 4.170A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 990 through 995 Processing helix chain 'B' and resid 996 through 1011 Processing helix chain 'B' and resid 1017 through 1034 removed outlier: 3.785A pdb=" N LYS B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1042 Processing helix chain 'B' and resid 1059 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.695A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.720A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.830A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 528 removed outlier: 4.431A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.528A pdb=" N GLU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 940 through 960 removed outlier: 4.714A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 987 through 993 Processing helix chain 'C' and resid 996 through 1011 Processing helix chain 'C' and resid 1016 through 1033 Processing helix chain 'C' and resid 1033 through 1041 Processing helix chain 'C' and resid 1059 through 1106 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'E' and resid 197 through 203 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 182 through 189 Processing helix chain 'G' and resid 197 through 203 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 189 Processing helix chain 'I' and resid 197 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 5.849A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.220A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 75 removed outlier: 4.151A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.088A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.429A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.989A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 232 through 235 Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 235 Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AB1, first strand: chain 'A' and resid 671 through 674 removed outlier: 3.836A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 367 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 405 removed outlier: 3.516A pdb=" N THR A 477 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.795A pdb=" N CYS A 585 " --> pdb=" O CYS A 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.335A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 780 Processing sheet with id=AB7, first strand: chain 'A' and resid 792 through 794 removed outlier: 7.308A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASN A1129 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.293A pdb=" N LEU B 318 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY B 115 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN B 114 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN B 258 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.189A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.148A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AC5, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AC7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC8, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AC9, first strand: chain 'B' and resid 359 through 363 removed outlier: 4.486A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.294A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.348A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP B 553 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD4, first strand: chain 'B' and resid 631 through 632 removed outlier: 3.560A pdb=" N TYR B 632 " --> pdb=" O THR C 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AD6, first strand: chain 'B' and resid 778 through 783 Processing sheet with id=AD7, first strand: chain 'B' and resid 793 through 794 removed outlier: 3.647A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 801 through 802 removed outlier: 4.767A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE1, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.158A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.573A pdb=" N THR C 257 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 264 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.332A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.454A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 126 through 129 removed outlier: 4.114A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AE7, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AE8, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AE9, first strand: chain 'C' and resid 360 through 366 removed outlier: 4.359A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 671 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 374 through 375 removed outlier: 6.132A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 400 through 405 removed outlier: 7.254A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 419 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 7.305A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 615 through 619 Processing sheet with id=AF5, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AF6, first strand: chain 'C' and resid 1121 through 1130 removed outlier: 6.036A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C1139 " --> pdb=" O VAL C1124 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.030A pdb=" N GLU D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 114 through 118 removed outlier: 4.680A pdb=" N ALA D 130 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 181 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER D 174 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.454A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.614A pdb=" N THR E 120 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 92 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA E 33 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 52 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR E 57 " --> pdb=" O ILE E 52 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.614A pdb=" N THR E 120 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 92 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR E 112 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AG7, first strand: chain 'E' and resid 131 through 133 removed outlier: 3.640A pdb=" N ASP E 155 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR E 187 " --> pdb=" O ASP E 155 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER E 188 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA E 179 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 190 " --> pdb=" O PHE E 177 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.537A pdb=" N LYS E 220 " --> pdb=" O CYS E 207 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.501A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.195A pdb=" N ALA F 130 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 181 " --> pdb=" O ALA F 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 138 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.351A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.747A pdb=" N THR G 120 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA G 33 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.747A pdb=" N THR G 120 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR G 112 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AH9, first strand: chain 'G' and resid 131 through 133 removed outlier: 3.637A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER G 188 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA G 179 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER G 190 " --> pdb=" O PHE G 177 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.663A pdb=" N THR G 216 " --> pdb=" O HIS G 211 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AI3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AI4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.533A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.721A pdb=" N ALA H 130 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.479A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AI8, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.708A pdb=" N THR I 120 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA I 33 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE I 52 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.708A pdb=" N THR I 120 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR I 112 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 131 through 133 Processing sheet with id=AJ2, first strand: chain 'I' and resid 131 through 133 removed outlier: 3.750A pdb=" N VAL I 195 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS I 151 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP I 155 " --> pdb=" O TYR I 187 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR I 187 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 162 through 165 1296 hydrogen bonds defined for protein. 3480 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: 16.74 Time building geometry restraints manager: 14.25 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: 6945 1.33 - 1.45: 9425 1.45 - 1.57: 20392 1.57 - 1.70: 0 1.70 - 1.82: 257 Bond restraints: 37019 Sorted by residual: bond pdb=" N SER A 65 " pdb=" CA SER A 65 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.49e+01 bond pdb=" N GLU B 252 " pdb=" CA GLU B 252 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.25e+01 bond pdb=" N ASP A1182 " pdb=" CA ASP A1182 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.22e+01 bond pdb=" N TYR G 103 " pdb=" CA TYR G 103 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.13e+01 bond pdb=" N TYR E 103 " pdb=" CA TYR E 103 " ideal model delta sigma weight residual 1.458 1.487 -0.028 6.30e-03 2.52e+04 2.00e+01 ... (remaining 37014 not shown) Histogram of bond angle deviations from ideal: 95.14 - 103.02: 203 103.02 - 110.89: 10802 110.89 - 118.77: 22865 118.77 - 126.64: 16220 126.64 - 134.51: 271 Bond angle restraints: 50361 Sorted by residual: angle pdb=" CA PRO I 158 " pdb=" N PRO I 158 " pdb=" CD PRO I 158 " ideal model delta sigma weight residual 112.00 97.23 14.77 1.40e+00 5.10e-01 1.11e+02 angle pdb=" C TYR A 606 " pdb=" CA TYR A 606 " pdb=" CB TYR A 606 " ideal model delta sigma weight residual 110.90 95.15 15.75 1.58e+00 4.01e-01 9.94e+01 angle pdb=" N VAL A1205 " pdb=" CA VAL A1205 " pdb=" C VAL A1205 " ideal model delta sigma weight residual 110.74 102.51 8.23 9.10e-01 1.21e+00 8.18e+01 angle pdb=" N GLY A 931 " pdb=" CA GLY A 931 " pdb=" C GLY A 931 " ideal model delta sigma weight residual 112.73 102.38 10.35 1.20e+00 6.94e-01 7.44e+01 angle pdb=" N VAL A 639 " pdb=" CA VAL A 639 " pdb=" C VAL A 639 " ideal model delta sigma weight residual 111.77 102.84 8.93 1.04e+00 9.25e-01 7.37e+01 ... (remaining 50356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 19742 16.70 - 33.39: 1579 33.39 - 50.09: 570 50.09 - 66.78: 130 66.78 - 83.48: 10 Dihedral angle restraints: 22031 sinusoidal: 8343 harmonic: 13688 Sorted by residual: dihedral pdb=" C PRO I 158 " pdb=" N PRO I 158 " pdb=" CA PRO I 158 " pdb=" CB PRO I 158 " ideal model delta harmonic sigma weight residual -120.70 -142.54 21.84 0 2.50e+00 1.60e-01 7.63e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -158.62 72.62 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS A 679 " pdb=" SG CYS A 679 " pdb=" SG CYS A 713 " pdb=" CB CYS A 713 " ideal model delta sinusoidal sigma weight residual 93.00 162.42 -69.42 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 22028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 5380 0.198 - 0.395: 287 0.395 - 0.593: 9 0.593 - 0.791: 0 0.791 - 0.989: 1 Chirality restraints: 5677 Sorted by residual: chirality pdb=" CA PRO I 158 " pdb=" N PRO I 158 " pdb=" C PRO I 158 " pdb=" CB PRO I 158 " both_signs ideal model delta sigma weight residual False 2.72 1.73 0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CA THR B 43 " pdb=" N THR B 43 " pdb=" C THR B 43 " pdb=" CB THR B 43 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA THR C 741 " pdb=" N THR C 741 " pdb=" C THR C 741 " pdb=" CB THR C 741 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.99e+00 ... (remaining 5674 not shown) Planarity restraints: 6486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BSER C 51 " 0.031 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" C BSER C 51 " -0.109 2.00e-02 2.50e+03 pdb=" O BSER C 51 " 0.041 2.00e-02 2.50e+03 pdb=" N LYS C 52 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASER C 51 " 0.029 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ASER C 51 " -0.104 2.00e-02 2.50e+03 pdb=" O ASER C 51 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS C 52 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE I 157 " 0.079 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO I 158 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO I 158 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO I 158 " 0.057 5.00e-02 4.00e+02 ... (remaining 6483 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 6 1.79 - 2.57: 62 2.57 - 3.35: 43525 3.35 - 4.12: 95324 4.12 - 4.90: 162126 Nonbonded interactions: 301043 Sorted by model distance: nonbonded pdb=" OG1 THR D 109 " pdb=" C ASP D 170 " model vdw 1.014 3.270 nonbonded pdb=" OG1 THR D 109 " pdb=" O ASP D 170 " model vdw 1.041 2.440 nonbonded pdb=" CB THR D 109 " pdb=" C ASP D 170 " model vdw 1.524 3.700 nonbonded pdb=" OG1 THR D 109 " pdb=" N SER D 171 " model vdw 1.626 2.520 nonbonded pdb=" CB THR D 109 " pdb=" O ASP D 170 " model vdw 1.719 3.470 ... (remaining 301038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 588 or r \ esid 597 through 698 or resid 711 through 915 or resid 927 through 1189 or resid \ 1193 through 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 376 or r \ esid 383 through 588 or resid 597 through 698 or resid 711 through 915 or resid \ 927 through 1174 or resid 1180 through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 376 or resid 383 through \ 1174 or resid 1180 through 1189 or resid 1193 through 1206)) } ncs_group { reference = (chain 'D' and (resid 1 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 212)) selection = (chain 'F' and (resid 1 through 104 or (resid 105 through 106 and (name N or nam \ e CA or name C or name O or name CB )) or resid 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 164 or (resid 16 \ 5 through 166 and (name N or name CA or name C or name O or name CB )) or resid \ 167 through 172 or (resid 173 and (name N or name CA or name C or name O or name \ CB )) or resid 174 through 212)) selection = (chain 'H' and (resid 1 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 104 or (resid 105 through 106 and ( \ name N or name CA or name C or name O or name CB )) or resid 107 or (resid 108 a \ nd (name N or name CA or name C or name O or name CB )) or resid 109 through 164 \ or (resid 165 through 166 and (name N or name CA or name C or name O or name CB \ )) or resid 167 through 172 or (resid 173 and (name N or name CA or name C or n \ ame O or name CB )) or resid 174 through 212)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 0.010 Normalize map: mean=0, sd=1: 1.580 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: 0.030 Extract box with map and model: 8.810 Check model and map are aligned: 0.530 Set scattering table: 0.300 Process input model: 97.970 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.210 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 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 : 0.013 0.052 37019 Z= 0.863 Angle : 1.554 15.753 50361 Z= 1.189 Chirality : 0.109 0.989 5677 Planarity : 0.004 0.110 6486 Dihedral : 14.161 83.480 13143 Min Nonbonded Distance : 1.014 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 1.01 % Allowed : 4.65 % Favored : 94.34 % Rotamer: Outliers : 9.26 % Allowed : 9.98 % Favored : 80.76 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.12), residues: 4650 helix: 3.58 (0.18), residues: 776 sheet: 2.02 (0.15), residues: 1136 loop : -0.64 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 106 HIS 0.010 0.001 HIS C1138 PHE 0.031 0.002 PHE B 895 TYR 0.036 0.002 TYR A 609 ARG 0.005 0.001 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 668 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6837 (p-80) REVERT: A 389 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7148 (tt) REVERT: A 402 LEU cc_start: 0.0602 (OUTLIER) cc_final: -0.0428 (tp) REVERT: A 428 ILE cc_start: 0.2337 (OUTLIER) cc_final: 0.2032 (tt) REVERT: A 600 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.4968 (tm) REVERT: A 939 MET cc_start: 0.8574 (mtt) cc_final: 0.8367 (mtt) REVERT: A 1155 LEU cc_start: 0.7310 (tp) cc_final: 0.6808 (tm) REVERT: A 1173 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8183 (pp) REVERT: A 1184 TRP cc_start: 0.3909 (OUTLIER) cc_final: 0.3201 (p-90) REVERT: B 33 VAL cc_start: 0.5000 (OUTLIER) cc_final: 0.4784 (m) REVERT: B 101 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5707 (p90) REVERT: B 169 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7592 (tp) REVERT: B 201 TYR cc_start: 0.5358 (OUTLIER) cc_final: 0.3375 (p90) REVERT: B 231 TYR cc_start: 0.3247 (m-80) cc_final: 0.2910 (m-80) REVERT: B 412 THR cc_start: 0.5084 (OUTLIER) cc_final: 0.4883 (p) REVERT: B 986 THR cc_start: 0.4910 (OUTLIER) cc_final: 0.4487 (p) REVERT: C 156 PHE cc_start: 0.5374 (m-80) cc_final: 0.5154 (m-80) REVERT: C 412 THR cc_start: 0.7086 (OUTLIER) cc_final: 0.6691 (m) REVERT: C 488 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6130 (mp) REVERT: C 553 TRP cc_start: 0.7600 (m100) cc_final: 0.7283 (m100) REVERT: C 616 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7720 (p) REVERT: C 718 VAL cc_start: 0.6622 (OUTLIER) cc_final: 0.6368 (t) REVERT: C 759 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6097 (pp) REVERT: C 1040 LEU cc_start: 0.6635 (mt) cc_final: 0.6428 (mt) REVERT: C 1054 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5861 (mt) REVERT: C 1165 ILE cc_start: 0.4268 (OUTLIER) cc_final: 0.4003 (pt) REVERT: C 1192 TYR cc_start: 0.4225 (OUTLIER) cc_final: 0.3502 (p90) REVERT: D 143 GLU cc_start: 0.6704 (pm20) cc_final: 0.6383 (mp0) REVERT: E 11 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.6873 (p) REVERT: F 183 LYS cc_start: 0.1037 (OUTLIER) cc_final: 0.0686 (tptt) REVERT: G 195 VAL cc_start: 0.2372 (OUTLIER) cc_final: 0.2061 (t) REVERT: H 142 ARG cc_start: 0.4744 (mmp-170) cc_final: 0.4175 (mmm160) REVERT: H 145 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.3891 (pptt) REVERT: H 183 LYS cc_start: 0.1959 (OUTLIER) cc_final: 0.1660 (mmtp) REVERT: I 11 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6781 (p) REVERT: I 100 MET cc_start: 0.7581 (ptm) cc_final: 0.7199 (ptp) REVERT: I 207 CYS cc_start: -0.0124 (OUTLIER) cc_final: -0.0805 (p) outliers start: 374 outliers final: 56 residues processed: 944 average time/residue: 1.1356 time to fit residues: 1350.2606 Evaluate side-chains 461 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 377 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 740 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 207 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 158 PRO Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 207 CYS Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 221 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 273 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN A 166 ASN A 208 HIS A 408 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 765 ASN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN A1023 GLN A1084 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 78 GLN B 91 HIS B 98 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 398 ASN B 410 ASN B 582 ASN B 627 GLN B 688 GLN B 719 ASN B 765 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN B 988 GLN ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1110 GLN B1145 ASN B1160 ASN B1201 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS C 346 GLN C 408 ASN C 475 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 GLN C 832 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1056 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN C1160 ASN D 34 ASN D 37 GLN D 79 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 115 GLN F 34 ASN F 37 GLN F 79 GLN F 138 ASN ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN G 115 GLN H 34 ASN H 79 GLN H 138 ASN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN I 115 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 37019 Z= 0.270 Angle : 0.744 12.846 50361 Z= 0.395 Chirality : 0.048 0.337 5677 Planarity : 0.005 0.162 6486 Dihedral : 7.088 59.579 5215 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.39 % Favored : 95.16 % Rotamer: Outliers : 5.57 % Allowed : 18.62 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 4650 helix: 2.16 (0.18), residues: 787 sheet: 1.47 (0.15), residues: 1198 loop : -0.93 (0.11), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 125 HIS 0.011 0.002 HIS B 208 PHE 0.031 0.002 PHE C 827 TYR 0.033 0.002 TYR D 49 ARG 0.014 0.001 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 396 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.5914 (m-80) REVERT: A 428 ILE cc_start: 0.1932 (OUTLIER) cc_final: 0.1294 (tt) REVERT: A 762 ILE cc_start: 0.6308 (tp) cc_final: 0.6078 (tp) REVERT: A 887 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7417 (mmt-90) REVERT: A 939 MET cc_start: 0.8646 (mtt) cc_final: 0.8125 (mtt) REVERT: A 1155 LEU cc_start: 0.7655 (tp) cc_final: 0.7251 (tm) REVERT: A 1184 TRP cc_start: 0.4415 (OUTLIER) cc_final: 0.3882 (p-90) REVERT: B 72 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: B 111 GLN cc_start: 0.8022 (pt0) cc_final: 0.7743 (pt0) REVERT: B 147 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6287 (p90) REVERT: B 201 TYR cc_start: 0.5758 (OUTLIER) cc_final: 0.3909 (p90) REVERT: B 281 PHE cc_start: 0.6605 (t80) cc_final: 0.6383 (t80) REVERT: B 412 THR cc_start: 0.5663 (OUTLIER) cc_final: 0.5409 (p) REVERT: B 517 LEU cc_start: 0.5504 (pp) cc_final: 0.5037 (mt) REVERT: B 985 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6327 (pt) REVERT: B 1064 ASP cc_start: 0.7703 (m-30) cc_final: 0.7250 (m-30) REVERT: C 306 ASP cc_start: 0.7782 (t0) cc_final: 0.7333 (t70) REVERT: C 401 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.5247 (ttp80) REVERT: C 553 TRP cc_start: 0.7649 (m100) cc_final: 0.7292 (m100) REVERT: C 576 GLN cc_start: 0.8083 (mt0) cc_final: 0.7860 (mt0) REVERT: C 718 VAL cc_start: 0.6929 (t) cc_final: 0.6669 (t) REVERT: C 792 GLN cc_start: 0.4661 (mm-40) cc_final: 0.4255 (pm20) REVERT: C 1054 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.5616 (mt) REVERT: C 1058 LEU cc_start: 0.3990 (mp) cc_final: 0.3178 (mt) REVERT: C 1192 TYR cc_start: 0.4250 (OUTLIER) cc_final: 0.3151 (p90) REVERT: E 104 ASP cc_start: 0.5968 (t0) cc_final: 0.5754 (t0) REVERT: F 4 MET cc_start: 0.6708 (mmm) cc_final: 0.6473 (mmm) REVERT: F 103 LYS cc_start: 0.7536 (mmmt) cc_final: 0.7253 (mppt) REVERT: G 181 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7080 (mm) REVERT: G 195 VAL cc_start: 0.2747 (OUTLIER) cc_final: 0.2323 (t) REVERT: H 145 LYS cc_start: 0.5064 (OUTLIER) cc_final: 0.4623 (pptt) REVERT: I 62 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8429 (pp30) outliers start: 225 outliers final: 71 residues processed: 580 average time/residue: 1.2122 time to fit residues: 879.5739 Evaluate side-chains 395 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 308 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1153 TYR Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 812 ASN Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 158 PRO Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 425 optimal weight: 6.9990 chunk 459 optimal weight: 6.9990 chunk 379 optimal weight: 40.0000 chunk 422 optimal weight: 50.0000 chunk 145 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 427 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN A 857 GLN A 974 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 544 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 HIS B 981 ASN C 98 GLN C 111 GLN C 258 GLN ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN C 857 GLN ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1063 GLN C1085 GLN C1129 ASN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 37 GLN ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 GLN I 6 GLN ** I 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 37019 Z= 0.442 Angle : 0.888 14.395 50361 Z= 0.478 Chirality : 0.053 0.336 5677 Planarity : 0.007 0.152 6486 Dihedral : 7.100 59.678 5139 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.78 % Favored : 92.73 % Rotamer: Outliers : 6.59 % Allowed : 18.90 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4650 helix: 0.87 (0.18), residues: 799 sheet: 0.81 (0.15), residues: 1225 loop : -1.43 (0.11), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP I 125 HIS 0.014 0.002 HIS A1138 PHE 0.046 0.003 PHE A 788 TYR 0.043 0.003 TYR B 287 ARG 0.016 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 350 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6391 (tp40) REVERT: A 389 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7244 (tt) REVERT: A 777 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.7134 (p90) REVERT: A 827 PHE cc_start: 0.6130 (m-10) cc_final: 0.5886 (m-10) REVERT: A 939 MET cc_start: 0.8371 (mtt) cc_final: 0.8104 (mtt) REVERT: A 1153 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 1183 GLU cc_start: 0.6377 (tp30) cc_final: 0.5364 (pm20) REVERT: A 1184 TRP cc_start: 0.5495 (OUTLIER) cc_final: 0.2696 (p-90) REVERT: A 1202 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6920 (t) REVERT: B 57 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8305 (tp) REVERT: B 72 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: B 201 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.4123 (p90) REVERT: B 226 ASN cc_start: 0.7615 (m-40) cc_final: 0.7169 (p0) REVERT: B 232 PHE cc_start: 0.2358 (OUTLIER) cc_final: 0.1689 (p90) REVERT: B 686 MET cc_start: 0.2548 (OUTLIER) cc_final: 0.1937 (pmm) REVERT: B 895 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8071 (t80) REVERT: B 1036 LEU cc_start: 0.7837 (tp) cc_final: 0.7602 (mt) REVERT: B 1064 ASP cc_start: 0.7694 (m-30) cc_final: 0.7305 (m-30) REVERT: B 1172 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.5984 (t80) REVERT: C 448 TYR cc_start: 0.6590 (t80) cc_final: 0.6351 (t80) REVERT: C 503 CYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7380 (t) REVERT: C 537 ASP cc_start: 0.7336 (p0) cc_final: 0.7039 (p0) REVERT: C 553 TRP cc_start: 0.7876 (m100) cc_final: 0.7565 (m100) REVERT: C 577 TYR cc_start: 0.4889 (m-10) cc_final: 0.4566 (m-80) REVERT: C 626 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7310 (ttm-80) REVERT: C 1040 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7825 (mm) REVERT: C 1054 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6114 (mt) REVERT: C 1058 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.3900 (mt) REVERT: C 1137 MET cc_start: 0.5505 (mpp) cc_final: 0.4557 (mpm) REVERT: C 1192 TYR cc_start: 0.4524 (OUTLIER) cc_final: 0.2837 (p90) REVERT: D 75 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7405 (tp) REVERT: E 10 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6021 (pp20) REVERT: F 106 ILE cc_start: 0.6570 (mp) cc_final: 0.6359 (mp) REVERT: G 10 GLU cc_start: 0.6994 (pp20) cc_final: 0.6645 (pp20) REVERT: G 181 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7218 (mm) REVERT: G 195 VAL cc_start: 0.2408 (OUTLIER) cc_final: 0.1722 (t) REVERT: H 32 TYR cc_start: 0.8187 (m-80) cc_final: 0.7756 (m-80) REVERT: H 173 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: I 62 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8323 (tm-30) outliers start: 266 outliers final: 97 residues processed: 570 average time/residue: 1.2506 time to fit residues: 889.0648 Evaluate side-chains 401 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 279 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1153 TYR Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1172 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 541 TYR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 812 ASN Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 50.0000 chunk 320 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 285 optimal weight: 6.9990 chunk 427 optimal weight: 20.0000 chunk 452 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 404 optimal weight: 0.9990 chunk 121 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 194 HIS A 208 HIS A 427 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 733 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1031 GLN B1129 ASN C 436 ASN C 792 GLN ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN D 6 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN F 34 ASN ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 37019 Z= 0.201 Angle : 0.694 13.299 50361 Z= 0.365 Chirality : 0.046 0.315 5677 Planarity : 0.005 0.139 6486 Dihedral : 6.293 59.688 5125 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.13 % Favored : 93.50 % Rotamer: Outliers : 4.46 % Allowed : 21.42 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4650 helix: 1.22 (0.18), residues: 792 sheet: 0.82 (0.14), residues: 1309 loop : -1.35 (0.11), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 125 HIS 0.005 0.001 HIS B 208 PHE 0.029 0.002 PHE C1191 TYR 0.034 0.002 TYR B 642 ARG 0.011 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 313 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7205 (tt) REVERT: A 939 MET cc_start: 0.8426 (mtt) cc_final: 0.8133 (mtt) REVERT: A 1012 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7509 (t80) REVERT: A 1153 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: A 1183 GLU cc_start: 0.5908 (tp30) cc_final: 0.5649 (pm20) REVERT: A 1184 TRP cc_start: 0.5080 (OUTLIER) cc_final: 0.3494 (p-90) REVERT: B 72 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: B 147 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6441 (p90) REVERT: B 201 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.3773 (p90) REVERT: B 517 LEU cc_start: 0.5409 (pp) cc_final: 0.5018 (mt) REVERT: B 686 MET cc_start: 0.2823 (OUTLIER) cc_final: 0.2216 (pmm) REVERT: B 1036 LEU cc_start: 0.7566 (tp) cc_final: 0.7281 (mt) REVERT: B 1064 ASP cc_start: 0.7788 (m-30) cc_final: 0.7392 (m-30) REVERT: B 1172 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: C 448 TYR cc_start: 0.6475 (t80) cc_final: 0.6179 (t80) REVERT: C 503 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7375 (t) REVERT: C 553 TRP cc_start: 0.8035 (m100) cc_final: 0.7597 (m100) REVERT: C 1040 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7579 (mm) REVERT: C 1054 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.5747 (mt) REVERT: C 1058 LEU cc_start: 0.4362 (OUTLIER) cc_final: 0.3824 (mt) REVERT: C 1192 TYR cc_start: 0.4287 (OUTLIER) cc_final: 0.2702 (p90) REVERT: C 1204 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5941 (m-10) REVERT: F 89 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6454 (pt0) REVERT: G 100 MET cc_start: 0.7876 (ptm) cc_final: 0.7524 (ptm) REVERT: G 195 VAL cc_start: 0.2209 (OUTLIER) cc_final: 0.1753 (t) REVERT: I 62 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (tm-30) outliers start: 180 outliers final: 73 residues processed: 459 average time/residue: 1.2382 time to fit residues: 707.5357 Evaluate side-chains 356 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 265 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1153 TYR Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1172 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 812 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain C residue 1204 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 125 TRP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 386 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 99 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 37019 Z= 0.271 Angle : 0.708 13.217 50361 Z= 0.372 Chirality : 0.046 0.306 5677 Planarity : 0.005 0.134 6486 Dihedral : 6.203 59.570 5119 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.12 % Favored : 92.51 % Rotamer: Outliers : 4.88 % Allowed : 21.67 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 4650 helix: 1.19 (0.19), residues: 788 sheet: 0.61 (0.15), residues: 1271 loop : -1.41 (0.11), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 125 HIS 0.007 0.001 HIS B1138 PHE 0.033 0.002 PHE I 157 TYR 0.032 0.002 TYR B 641 ARG 0.012 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 282 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7811 (mtm) cc_final: 0.7378 (mtm) REVERT: A 389 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7170 (tt) REVERT: A 777 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.7186 (p90) REVERT: A 788 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6403 (p90) REVERT: A 939 MET cc_start: 0.8450 (mtt) cc_final: 0.8152 (mtt) REVERT: A 1012 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 1153 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: A 1183 GLU cc_start: 0.6105 (tp30) cc_final: 0.5497 (pm20) REVERT: A 1184 TRP cc_start: 0.5038 (OUTLIER) cc_final: 0.3398 (p-90) REVERT: B 147 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6549 (p90) REVERT: B 167 HIS cc_start: 0.2220 (t70) cc_final: 0.1739 (m-70) REVERT: B 201 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.3648 (p90) REVERT: B 412 THR cc_start: 0.5548 (OUTLIER) cc_final: 0.5346 (p) REVERT: B 569 MET cc_start: 0.4888 (mpm) cc_final: 0.4668 (mpm) REVERT: B 686 MET cc_start: 0.2801 (pmm) cc_final: 0.2385 (pmm) REVERT: B 793 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: B 1064 ASP cc_start: 0.7710 (m-30) cc_final: 0.7299 (m-30) REVERT: B 1172 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.5803 (t80) REVERT: C 553 TRP cc_start: 0.7995 (m100) cc_final: 0.7545 (m100) REVERT: C 728 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7353 (tppt) REVERT: C 1040 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7696 (mm) REVERT: C 1054 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.5913 (mt) REVERT: C 1058 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4165 (mt) REVERT: C 1164 CYS cc_start: 0.6582 (OUTLIER) cc_final: 0.5957 (t) REVERT: C 1192 TYR cc_start: 0.4719 (OUTLIER) cc_final: 0.3047 (p90) REVERT: C 1204 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5984 (m-10) REVERT: E 81 MET cc_start: 0.7329 (tmt) cc_final: 0.6879 (tmt) REVERT: E 95 TYR cc_start: 0.7914 (m-80) cc_final: 0.7656 (m-80) REVERT: E 98 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7206 (tmm160) REVERT: F 4 MET cc_start: 0.6718 (mmm) cc_final: 0.6464 (mmm) REVERT: F 89 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6458 (pt0) REVERT: F 105 GLU cc_start: 0.5205 (tm-30) cc_final: 0.5003 (tm-30) REVERT: F 106 ILE cc_start: 0.6316 (mp) cc_final: 0.5906 (mt) REVERT: G 100 MET cc_start: 0.7878 (ptm) cc_final: 0.7601 (ptm) REVERT: G 195 VAL cc_start: 0.2229 (OUTLIER) cc_final: 0.1801 (t) REVERT: H 106 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6514 (mp) REVERT: H 173 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7070 (m-10) REVERT: I 62 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8294 (tm-30) outliers start: 197 outliers final: 96 residues processed: 446 average time/residue: 1.2677 time to fit residues: 705.4533 Evaluate side-chains 376 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 258 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1153 TYR Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1172 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 812 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain C residue 1204 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 151 CYS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 0.9980 chunk 407 optimal weight: 5.9990 chunk 89 optimal weight: 0.0370 chunk 265 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 452 optimal weight: 7.9990 chunk 375 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS C1138 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 37019 Z= 0.251 Angle : 0.695 12.978 50361 Z= 0.364 Chirality : 0.045 0.292 5677 Planarity : 0.005 0.136 6486 Dihedral : 6.129 59.231 5118 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.27 % Favored : 92.36 % Rotamer: Outliers : 4.43 % Allowed : 22.31 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4650 helix: 1.29 (0.19), residues: 777 sheet: 0.62 (0.15), residues: 1285 loop : -1.44 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 125 HIS 0.006 0.001 HIS B1138 PHE 0.033 0.002 PHE B 183 TYR 0.033 0.002 TYR F 49 ARG 0.011 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 287 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: A 258 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: A 738 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6264 (tp) REVERT: A 777 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.7036 (p90) REVERT: A 939 MET cc_start: 0.8412 (mtt) cc_final: 0.8118 (mtt) REVERT: A 988 GLN cc_start: 0.4022 (OUTLIER) cc_final: 0.3421 (tt0) REVERT: A 1012 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7538 (t80) REVERT: A 1153 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: A 1183 GLU cc_start: 0.6025 (tp30) cc_final: 0.5722 (pm20) REVERT: A 1184 TRP cc_start: 0.5207 (OUTLIER) cc_final: 0.3411 (p-90) REVERT: B 147 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6629 (p90) REVERT: B 226 ASN cc_start: 0.7759 (m-40) cc_final: 0.6908 (p0) REVERT: B 240 MET cc_start: 0.7336 (tmt) cc_final: 0.6924 (tmm) REVERT: B 569 MET cc_start: 0.5081 (mpm) cc_final: 0.4860 (mpm) REVERT: B 686 MET cc_start: 0.3074 (pmm) cc_final: 0.2293 (pmm) REVERT: B 793 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: B 967 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6806 (p90) REVERT: B 1064 ASP cc_start: 0.7728 (m-30) cc_final: 0.7343 (m-30) REVERT: B 1172 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.5870 (t80) REVERT: C 258 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6017 (tp40) REVERT: C 553 TRP cc_start: 0.8006 (m100) cc_final: 0.7465 (m100) REVERT: C 576 GLN cc_start: 0.7999 (mt0) cc_final: 0.7691 (pt0) REVERT: C 1040 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7732 (mm) REVERT: C 1054 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.5953 (mt) REVERT: C 1058 LEU cc_start: 0.4815 (OUTLIER) cc_final: 0.4350 (mt) REVERT: C 1164 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6100 (t) REVERT: C 1192 TYR cc_start: 0.4396 (OUTLIER) cc_final: 0.3411 (p90) REVERT: C 1204 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.6020 (m-10) REVERT: E 81 MET cc_start: 0.7401 (tmt) cc_final: 0.6983 (tmt) REVERT: E 95 TYR cc_start: 0.7956 (m-80) cc_final: 0.7680 (m-80) REVERT: F 89 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6620 (pt0) REVERT: F 106 ILE cc_start: 0.6281 (mp) cc_final: 0.5972 (mt) REVERT: G 89 GLU cc_start: 0.8265 (pm20) cc_final: 0.8005 (pm20) REVERT: G 100 MET cc_start: 0.7931 (ptm) cc_final: 0.7686 (ptm) REVERT: H 173 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: I 62 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8275 (tm-30) outliers start: 179 outliers final: 96 residues processed: 433 average time/residue: 1.2578 time to fit residues: 679.2502 Evaluate side-chains 377 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 259 time to evaluate : 4.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1153 TYR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1172 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 812 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain C residue 1204 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 151 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 381 optimal weight: 30.0000 chunk 252 optimal weight: 0.7980 chunk 451 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 576 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN B 842 GLN B 988 GLN B1132 ASN C 519 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 GLN C1138 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN G 6 GLN G 208 ASN H 34 ASN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 37019 Z= 0.360 Angle : 0.779 13.864 50361 Z= 0.410 Chirality : 0.048 0.284 5677 Planarity : 0.006 0.136 6486 Dihedral : 6.376 56.609 5114 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.35 % Favored : 91.24 % Rotamer: Outliers : 5.10 % Allowed : 22.24 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4650 helix: 1.06 (0.19), residues: 778 sheet: 0.50 (0.15), residues: 1301 loop : -1.59 (0.11), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 125 HIS 0.009 0.002 HIS C 91 PHE 0.043 0.003 PHE G 157 TYR 0.043 0.003 TYR B 641 ARG 0.016 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 272 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: A 788 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6466 (p90) REVERT: A 913 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7476 (mpt) REVERT: A 939 MET cc_start: 0.8324 (mtt) cc_final: 0.8030 (mtt) REVERT: A 988 GLN cc_start: 0.4364 (OUTLIER) cc_final: 0.3801 (tt0) REVERT: A 1012 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 1184 TRP cc_start: 0.5669 (OUTLIER) cc_final: 0.4204 (p-90) REVERT: B 183 PHE cc_start: 0.6994 (p90) cc_final: 0.6584 (p90) REVERT: B 232 PHE cc_start: 0.2189 (OUTLIER) cc_final: 0.1006 (p90) REVERT: B 281 PHE cc_start: 0.6632 (t80) cc_final: 0.6310 (t80) REVERT: B 401 ARG cc_start: 0.4025 (tpp-160) cc_final: 0.3817 (tpp-160) REVERT: B 686 MET cc_start: 0.4792 (pmm) cc_final: 0.4589 (pmm) REVERT: B 793 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: B 967 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7094 (p90) REVERT: B 1036 LEU cc_start: 0.7436 (mt) cc_final: 0.7135 (mt) REVERT: B 1064 ASP cc_start: 0.7598 (m-30) cc_final: 0.7208 (m-30) REVERT: B 1204 TYR cc_start: 0.5248 (OUTLIER) cc_final: 0.4397 (t80) REVERT: C 258 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6027 (tp40) REVERT: C 553 TRP cc_start: 0.7994 (m100) cc_final: 0.7456 (m100) REVERT: C 576 GLN cc_start: 0.8024 (mt0) cc_final: 0.7733 (pt0) REVERT: C 865 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6461 (m-10) REVERT: C 906 MET cc_start: 0.2303 (tpt) cc_final: 0.2071 (tpt) REVERT: C 1040 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7984 (mm) REVERT: C 1054 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6124 (mt) REVERT: C 1055 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6746 (tp) REVERT: C 1058 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4530 (mt) REVERT: C 1075 LEU cc_start: 0.7224 (mt) cc_final: 0.6865 (pp) REVERT: C 1137 MET cc_start: 0.7281 (mpm) cc_final: 0.6909 (mpm) REVERT: C 1171 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6501 (t80) REVERT: C 1192 TYR cc_start: 0.5330 (OUTLIER) cc_final: 0.3874 (p90) REVERT: E 95 TYR cc_start: 0.7920 (m-80) cc_final: 0.7615 (m-80) REVERT: F 89 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7010 (pt0) REVERT: F 106 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.6136 (mt) REVERT: G 89 GLU cc_start: 0.8389 (pm20) cc_final: 0.8172 (pm20) REVERT: G 187 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: H 103 LYS cc_start: 0.7458 (mmpt) cc_final: 0.7249 (mmmt) REVERT: H 173 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: H 183 LYS cc_start: 0.2079 (OUTLIER) cc_final: 0.1718 (mmpt) REVERT: I 62 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: I 82 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7600 (tm-30) REVERT: I 157 PHE cc_start: 0.5548 (OUTLIER) cc_final: 0.5123 (m-80) REVERT: I 187 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5408 (m-10) outliers start: 206 outliers final: 104 residues processed: 442 average time/residue: 1.3220 time to fit residues: 724.4543 Evaluate side-chains 373 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 243 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1171 TYR Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 151 CYS Chi-restraints excluded: chain G residue 187 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 157 PHE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 187 TYR Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 269 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 307 optimal weight: 0.0670 chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 354 optimal weight: 40.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN B 842 GLN B 988 GLN B1023 GLN B1056 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 GLN C1145 ASN D 6 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 37 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 37019 Z= 0.197 Angle : 0.706 14.122 50361 Z= 0.364 Chirality : 0.045 0.340 5677 Planarity : 0.005 0.134 6486 Dihedral : 5.931 56.114 5110 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.08 % Favored : 92.49 % Rotamer: Outliers : 3.39 % Allowed : 24.22 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4650 helix: 1.23 (0.19), residues: 787 sheet: 0.56 (0.15), residues: 1340 loop : -1.57 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 125 HIS 0.007 0.001 HIS C 194 PHE 0.033 0.002 PHE B 183 TYR 0.033 0.002 TYR B 641 ARG 0.010 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 265 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 TYR cc_start: 0.7260 (p90) cc_final: 0.6804 (p90) REVERT: A 939 MET cc_start: 0.8336 (mtt) cc_final: 0.8058 (mtt) REVERT: A 1012 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8172 (t80) REVERT: A 1184 TRP cc_start: 0.5056 (OUTLIER) cc_final: 0.3617 (p-90) REVERT: B 183 PHE cc_start: 0.7008 (p90) cc_final: 0.6647 (p90) REVERT: B 240 MET cc_start: 0.7377 (tmt) cc_final: 0.6987 (tmm) REVERT: B 281 PHE cc_start: 0.6575 (t80) cc_final: 0.6245 (t80) REVERT: B 569 MET cc_start: 0.5231 (mpm) cc_final: 0.4994 (mpm) REVERT: B 793 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: B 1064 ASP cc_start: 0.7700 (m-30) cc_final: 0.7311 (m-30) REVERT: C 553 TRP cc_start: 0.7936 (m100) cc_final: 0.7423 (m100) REVERT: C 576 GLN cc_start: 0.7970 (mt0) cc_final: 0.7716 (pt0) REVERT: C 865 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.6195 (m-10) REVERT: C 1040 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7800 (mm) REVERT: C 1054 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6102 (mt) REVERT: C 1058 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4721 (mt) REVERT: C 1075 LEU cc_start: 0.7078 (mt) cc_final: 0.6763 (pp) REVERT: C 1137 MET cc_start: 0.7008 (mpm) cc_final: 0.6673 (mpm) REVERT: C 1192 TYR cc_start: 0.5256 (OUTLIER) cc_final: 0.4001 (p90) REVERT: E 95 TYR cc_start: 0.7992 (m-80) cc_final: 0.7723 (m-80) REVERT: F 4 MET cc_start: 0.6736 (mmm) cc_final: 0.6144 (mmp) REVERT: F 89 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6717 (pt0) REVERT: F 106 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5867 (mt) REVERT: G 187 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6747 (m-80) REVERT: H 183 LYS cc_start: 0.2054 (OUTLIER) cc_final: 0.1685 (mmpt) REVERT: I 62 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: I 82 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7499 (tm-30) outliers start: 137 outliers final: 80 residues processed: 379 average time/residue: 1.2931 time to fit residues: 604.8155 Evaluate side-chains 330 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 237 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 541 TYR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 151 CYS Chi-restraints excluded: chain G residue 187 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 8.9990 chunk 432 optimal weight: 8.9990 chunk 394 optimal weight: 50.0000 chunk 420 optimal weight: 40.0000 chunk 253 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 330 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 379 optimal weight: 6.9990 chunk 397 optimal weight: 0.6980 chunk 418 optimal weight: 50.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 319 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN C 519 ASN C 792 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 GLN C1145 ASN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN H 34 ASN H 37 GLN I 62 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.6931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 37019 Z= 0.373 Angle : 0.801 14.181 50361 Z= 0.418 Chirality : 0.049 0.353 5677 Planarity : 0.006 0.132 6486 Dihedral : 6.305 57.092 5108 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.48 % Favored : 91.09 % Rotamer: Outliers : 3.57 % Allowed : 24.27 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4650 helix: 0.93 (0.19), residues: 788 sheet: 0.37 (0.15), residues: 1308 loop : -1.67 (0.11), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B1184 HIS 0.014 0.002 HIS C1138 PHE 0.048 0.003 PHE I 133 TYR 0.054 0.002 TYR B 641 ARG 0.019 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 249 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6221 (tp40) REVERT: A 913 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7365 (mpt) REVERT: A 939 MET cc_start: 0.8292 (mtt) cc_final: 0.8040 (mtt) REVERT: A 1012 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7828 (t80) REVERT: A 1184 TRP cc_start: 0.4745 (OUTLIER) cc_final: 0.3189 (p-90) REVERT: B 84 MET cc_start: 0.8367 (ttt) cc_final: 0.7977 (ttt) REVERT: B 183 PHE cc_start: 0.7357 (p90) cc_final: 0.7035 (p90) REVERT: B 269 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6549 (ptp-170) REVERT: B 281 PHE cc_start: 0.6680 (t80) cc_final: 0.6474 (t80) REVERT: B 569 MET cc_start: 0.5340 (mpm) cc_final: 0.5032 (mpm) REVERT: B 793 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: B 967 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6891 (p90) REVERT: B 1064 ASP cc_start: 0.7535 (m-30) cc_final: 0.7148 (m-30) REVERT: C 553 TRP cc_start: 0.7959 (m100) cc_final: 0.7546 (m100) REVERT: C 576 GLN cc_start: 0.7992 (mt0) cc_final: 0.7724 (pt0) REVERT: C 757 MET cc_start: 0.6929 (mtm) cc_final: 0.6722 (ttp) REVERT: C 865 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: C 1040 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8081 (mm) REVERT: C 1054 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6248 (mp) REVERT: C 1058 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4734 (mt) REVERT: C 1137 MET cc_start: 0.7932 (mpm) cc_final: 0.7550 (mpm) REVERT: C 1192 TYR cc_start: 0.5448 (OUTLIER) cc_final: 0.4019 (p90) REVERT: E 95 TYR cc_start: 0.7980 (m-80) cc_final: 0.7688 (m-80) REVERT: F 89 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: F 107 LYS cc_start: 0.7355 (mtmt) cc_final: 0.7089 (mtmm) REVERT: G 187 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: H 125 LEU cc_start: 0.4398 (OUTLIER) cc_final: 0.3779 (mt) REVERT: H 183 LYS cc_start: 0.2110 (OUTLIER) cc_final: 0.1682 (mmtt) REVERT: I 62 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: I 82 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7615 (tm-30) REVERT: I 187 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.5411 (m-10) outliers start: 144 outliers final: 91 residues processed: 369 average time/residue: 1.2827 time to fit residues: 589.1236 Evaluate side-chains 339 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 230 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 151 CYS Chi-restraints excluded: chain G residue 187 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 187 TYR Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 5.9990 chunk 444 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 308 optimal weight: 0.0980 chunk 466 optimal weight: 30.0000 chunk 429 optimal weight: 0.9980 chunk 371 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 286 optimal weight: 0.5980 chunk 227 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 319 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN C 436 ASN C 519 ASN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 GLN C1145 ASN D 79 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN H 37 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 37019 Z= 0.197 Angle : 0.726 14.602 50361 Z= 0.373 Chirality : 0.045 0.354 5677 Planarity : 0.005 0.131 6486 Dihedral : 5.886 56.796 5106 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.21 % Favored : 92.36 % Rotamer: Outliers : 2.85 % Allowed : 25.11 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 4650 helix: 1.17 (0.19), residues: 796 sheet: 0.41 (0.15), residues: 1316 loop : -1.66 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B1184 HIS 0.008 0.001 HIS A1146 PHE 0.040 0.002 PHE I 133 TYR 0.033 0.002 TYR B 641 ARG 0.014 0.001 ARG H 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 260 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6443 (tp40) REVERT: A 452 MET cc_start: 0.0879 (mtm) cc_final: -0.0670 (ttt) REVERT: A 777 TYR cc_start: 0.7320 (p90) cc_final: 0.6840 (p90) REVERT: A 913 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7416 (mpt) REVERT: A 939 MET cc_start: 0.8282 (mtt) cc_final: 0.8008 (mtt) REVERT: A 1184 TRP cc_start: 0.4744 (OUTLIER) cc_final: 0.3523 (p-90) REVERT: B 48 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7931 (tt) REVERT: B 183 PHE cc_start: 0.7224 (p90) cc_final: 0.6833 (p90) REVERT: B 187 LEU cc_start: 0.4843 (pt) cc_final: 0.4462 (mt) REVERT: B 240 MET cc_start: 0.7348 (tmt) cc_final: 0.6975 (tmm) REVERT: B 793 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: B 1064 ASP cc_start: 0.7646 (m-30) cc_final: 0.7275 (m-30) REVERT: C 427 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6905 (tt0) REVERT: C 553 TRP cc_start: 0.7900 (m100) cc_final: 0.7490 (m100) REVERT: C 576 GLN cc_start: 0.7910 (mt0) cc_final: 0.7650 (pt0) REVERT: C 865 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6387 (m-10) REVERT: C 1040 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7781 (mm) REVERT: C 1054 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6281 (mt) REVERT: C 1075 LEU cc_start: 0.7224 (mt) cc_final: 0.6826 (pp) REVERT: C 1137 MET cc_start: 0.7609 (mpm) cc_final: 0.7341 (mpm) REVERT: C 1192 TYR cc_start: 0.5126 (OUTLIER) cc_final: 0.4039 (p90) REVERT: D 32 TYR cc_start: 0.8126 (m-80) cc_final: 0.7807 (m-80) REVERT: E 95 TYR cc_start: 0.8079 (m-80) cc_final: 0.7699 (m-80) REVERT: F 4 MET cc_start: 0.6800 (mmm) cc_final: 0.6114 (mmp) REVERT: F 89 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: G 187 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6855 (m-80) REVERT: H 125 LEU cc_start: 0.4485 (OUTLIER) cc_final: 0.3788 (mt) REVERT: H 183 LYS cc_start: 0.1897 (OUTLIER) cc_final: 0.1486 (mmtt) REVERT: I 82 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7446 (tm-30) outliers start: 115 outliers final: 70 residues processed: 354 average time/residue: 1.3632 time to fit residues: 593.3285 Evaluate side-chains 330 residues out of total 4044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 247 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 TRP Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1160 ASN Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1172 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 151 CYS Chi-restraints excluded: chain G residue 187 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 5.9990 chunk 395 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 371 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 381 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 796 GLN B 808 GLN ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN C 519 ASN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN D 199 GLN F 37 GLN H 37 GLN ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.122573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.091399 restraints weight = 141362.172| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 4.01 r_work: 0.3535 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 37019 Z= 0.467 Angle : 0.854 14.819 50361 Z= 0.448 Chirality : 0.050 0.297 5677 Planarity : 0.006 0.131 6486 Dihedral : 6.445 58.997 5105 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.61 % Favored : 90.94 % Rotamer: Outliers : 3.22 % Allowed : 24.86 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.04 (0.12), residues: 4650 helix: 0.79 (0.19), residues: 789 sheet: 0.19 (0.15), residues: 1298 loop : -1.72 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B1184 HIS 0.014 0.002 HIS C1138 PHE 0.048 0.003 PHE I 133 TYR 0.059 0.003 TYR B 641 ARG 0.021 0.001 ARG C1179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13734.51 seconds wall clock time: 246 minutes 2.47 seconds (14762.47 seconds total)