Starting phenix.real_space_refine on Sat Feb 17 09:20:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qle_4580/02_2024/6qle_4580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qle_4580/02_2024/6qle_4580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qle_4580/02_2024/6qle_4580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qle_4580/02_2024/6qle_4580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qle_4580/02_2024/6qle_4580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qle_4580/02_2024/6qle_4580.pdb" } resolution = 3.55 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. 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 76 5.16 5 C 11655 2.51 5 N 3146 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 389": "OD1" <-> "OD2" Residue "I PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 488": "OD1" <-> "OD2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K ARG 119": "NH1" <-> "NH2" Residue "L ASP 45": "OD1" <-> "OD2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 186": "OD1" <-> "OD2" Residue "L TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 9": "OD1" <-> "OD2" Residue "N TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "N TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 93": "OD1" <-> "OD2" Residue "N ASP 135": "OD1" <-> "OD2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 285": "OD1" <-> "OD2" Residue "N PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 408": "OD1" <-> "OD2" Residue "N ASP 425": "OD1" <-> "OD2" Residue "N PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 162": "OD1" <-> "OD2" Residue "O ASP 185": "OD1" <-> "OD2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 312": "OD1" <-> "OD2" Residue "O GLU 316": "OE1" <-> "OE2" Residue "O GLU 323": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 246": "OE1" <-> "OE2" Residue "Q PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 233": "OD1" <-> "OD2" Residue "Q TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 264": "NH1" <-> "NH2" Residue "Q ASP 338": "OD1" <-> "OD2" Residue "Q GLU 372": "OE1" <-> "OE2" Residue "U ARG 187": "NH1" <-> "NH2" Residue "U ARG 212": "NH1" <-> "NH2" Residue "U ASP 215": "OD1" <-> "OD2" Residue "U ASP 248": "OD1" <-> "OD2" Residue "U ASP 286": "OD1" <-> "OD2" Residue "U PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Z TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18162 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2699 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 8 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 5, 'TYR:plan': 3, 'UNK:plan-1': 24, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 157 Chain: "K" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 774 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2922 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1865 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "Q" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1584 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 15, 'ASP:plan': 6, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "U" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1231 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'UNK:plan-1': 26, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 10.28, per 1000 atoms: 0.57 Number of scatterers: 18162 At special positions: 0 Unit cell: (184.21, 173.31, 131.89, 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 76 16.00 O 3285 8.00 N 3146 7.00 C 11655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.43 Conformation dependent library (CDL) restraints added in 3.3 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 64.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'H' and resid 5 through 39 removed outlier: 4.092A pdb=" N HIS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 73 Processing helix chain 'H' and resid 83 through 94 removed outlier: 4.377A pdb=" N ASN H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 135 Processing helix chain 'I' and resid 323 through 328 removed outlier: 3.672A pdb=" N UNK I 327 " --> pdb=" O UNK I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 339 removed outlier: 4.207A pdb=" N LEU I 339 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 350 removed outlier: 4.401A pdb=" N ILE I 346 " --> pdb=" O SER I 342 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 374 through 377 removed outlier: 3.562A pdb=" N GLU I 377 " --> pdb=" O THR I 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 374 through 377' Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.639A pdb=" N CYS I 401 " --> pdb=" O ILE I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 421 Processing helix chain 'I' and resid 422 through 424 No H-bonds generated for 'chain 'I' and resid 422 through 424' Processing helix chain 'I' and resid 431 through 448 removed outlier: 4.108A pdb=" N PHE I 435 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE I 444 " --> pdb=" O MET I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 473 removed outlier: 3.892A pdb=" N THR I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 493 Processing helix chain 'I' and resid 506 through 524 Processing helix chain 'I' and resid 538 through 548 Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 576 through 592 Processing helix chain 'I' and resid 607 through 619 removed outlier: 3.937A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR I 619 " --> pdb=" O LEU I 615 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 653 Processing helix chain 'I' and resid 666 through 675 removed outlier: 3.731A pdb=" N UNK I 670 " --> pdb=" O UNK I 666 " (cutoff:3.500A) Processing helix chain 'I' and resid 693 through 707 removed outlier: 3.898A pdb=" N ARG I 697 " --> pdb=" O ILE I 693 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL I 698 " --> pdb=" O HIS I 694 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR I 707 " --> pdb=" O HIS I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 721 Processing helix chain 'I' and resid 722 through 726 Processing helix chain 'K' and resid 8 through 40 Processing helix chain 'K' and resid 51 through 59 removed outlier: 3.656A pdb=" N LYS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 128 Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.564A pdb=" N TYR L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 127 Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.704A pdb=" N LYS L 156 " --> pdb=" O THR L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.566A pdb=" N ASP L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 197 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.591A pdb=" N ILE L 240 " --> pdb=" O VAL L 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 3.654A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.602A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 3.736A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 65 Processing helix chain 'N' and resid 67 through 77 removed outlier: 3.971A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 3.613A pdb=" N LEU N 89 " --> pdb=" O ASN N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.836A pdb=" N PHE N 104 " --> pdb=" O PRO N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 126 through 137 removed outlier: 4.184A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.771A pdb=" N ARG N 222 " --> pdb=" O ASP N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 removed outlier: 3.934A pdb=" N ILE N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 265 removed outlier: 4.339A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 257 removed outlier: 3.950A pdb=" N LEU O 257 " --> pdb=" O ASN O 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 254 through 257' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.731A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 349 removed outlier: 3.709A pdb=" N TRP O 344 " --> pdb=" O ASN O 340 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU O 349 " --> pdb=" O GLU O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 359 removed outlier: 3.709A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 109 Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.749A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 230 through 234 removed outlier: 3.763A pdb=" N ALA P 233 " --> pdb=" O GLN P 230 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR P 234 " --> pdb=" O LEU P 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 230 through 234' Processing helix chain 'P' and resid 236 through 264 Processing helix chain 'P' and resid 333 through 348 removed outlier: 3.735A pdb=" N TYR P 348 " --> pdb=" O LEU P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 363 Processing helix chain 'Q' and resid 126 through 137 removed outlier: 3.995A pdb=" N UNK Q 130 " --> pdb=" O UNK Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 187 Processing helix chain 'Q' and resid 193 through 217 Processing helix chain 'Q' and resid 233 through 291 Processing helix chain 'Q' and resid 323 through 332 Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.239A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP Q 380 " --> pdb=" O GLN Q 376 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER Q 381 " --> pdb=" O MET Q 377 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 387 Processing helix chain 'U' and resid 132 through 156 Processing helix chain 'U' and resid 167 through 231 removed outlier: 4.981A pdb=" N LEU U 173 " --> pdb=" O LEU U 169 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU U 175 " --> pdb=" O TYR U 171 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN U 200 " --> pdb=" O ASN U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.519A pdb=" N HIS U 237 " --> pdb=" O GLY U 233 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 321 removed outlier: 3.616A pdb=" N LEU U 320 " --> pdb=" O LEU U 316 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.778A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 removed outlier: 3.782A pdb=" N LEU Y 30 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA Y 31 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 57 through 82 removed outlier: 3.887A pdb=" N SER Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN Y 77 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 102 removed outlier: 3.755A pdb=" N ARG Y 98 " --> pdb=" O GLY Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 118 Processing helix chain 'Y' and resid 137 through 186 removed outlier: 3.547A pdb=" N GLU Y 186 " --> pdb=" O LYS Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 217 removed outlier: 5.286A pdb=" N ASN Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY Y 199 " --> pdb=" O ALA Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 237 Processing helix chain 'Z' and resid 4 through 14 removed outlier: 3.828A pdb=" N ASN Z 9 " --> pdb=" O GLN Z 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER Z 14 " --> pdb=" O TYR Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 19 removed outlier: 3.951A pdb=" N THR Z 18 " --> pdb=" O LEU Z 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Z 19 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 15 through 19' Processing helix chain 'Z' and resid 37 through 83 Processing helix chain 'Z' and resid 88 through 124 removed outlier: 3.697A pdb=" N ASN Z 124 " --> pdb=" O ALA Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 152 Processing sheet with id=AA1, first strand: chain 'L' and resid 73 through 76 removed outlier: 3.961A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 31 through 33 removed outlier: 3.964A pdb=" N ASP L 32 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG L 59 " --> pdb=" O ASP L 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=AA4, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA5, first strand: chain 'N' and resid 141 through 148 removed outlier: 4.265A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 141 through 148 removed outlier: 4.265A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 295 through 298 removed outlier: 3.756A pdb=" N LYS N 295 " --> pdb=" O ILE P 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 397 through 400 removed outlier: 7.027A pdb=" N THR N 388 " --> pdb=" O ILE N 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 175 through 180 removed outlier: 3.510A pdb=" N THR O 176 " --> pdb=" O ARG O 205 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 186 through 188 removed outlier: 3.502A pdb=" N LYS O 187 " --> pdb=" O PHE O 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 305 through 309 removed outlier: 3.813A pdb=" N LYS O 314 " --> pdb=" O LEU O 330 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 168 through 172 removed outlier: 3.526A pdb=" N SER P 168 " --> pdb=" O ASN P 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN P 186 " --> pdb=" O SER P 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG P 172 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL P 182 " --> pdb=" O ARG P 172 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 270 through 272 removed outlier: 3.538A pdb=" N TYR P 272 " --> pdb=" O ILE P 281 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5704 1.34 - 1.46: 3046 1.46 - 1.58: 9550 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 18425 Sorted by residual: bond pdb=" CG1 ILE O 240 " pdb=" CD1 ILE O 240 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" C VAL L 40 " pdb=" N PRO L 41 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CA GLY Y 220 " pdb=" C GLY Y 220 " ideal model delta sigma weight residual 1.511 1.530 -0.019 1.25e-02 6.40e+03 2.34e+00 bond pdb=" N GLY Y 220 " pdb=" CA GLY Y 220 " ideal model delta sigma weight residual 1.453 1.473 -0.020 1.43e-02 4.89e+03 2.01e+00 bond pdb=" CB VAL I 545 " pdb=" CG2 VAL I 545 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 ... (remaining 18420 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.07: 287 106.07 - 113.13: 10340 113.13 - 120.19: 6872 120.19 - 127.26: 7315 127.26 - 134.32: 135 Bond angle restraints: 24949 Sorted by residual: angle pdb=" N PRO Y 223 " pdb=" CA PRO Y 223 " pdb=" CB PRO Y 223 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.43e+01 angle pdb=" N PRO H 136 " pdb=" CA PRO H 136 " pdb=" CB PRO H 136 " ideal model delta sigma weight residual 103.00 110.28 -7.28 1.10e+00 8.26e-01 4.38e+01 angle pdb=" N PRO Z 137 " pdb=" CA PRO Z 137 " pdb=" CB PRO Z 137 " ideal model delta sigma weight residual 103.44 110.08 -6.64 1.12e+00 7.97e-01 3.52e+01 angle pdb=" C THR I 574 " pdb=" N ASN I 575 " pdb=" CA ASN I 575 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C GLU L 135 " pdb=" N ASN L 136 " pdb=" CA ASN L 136 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 ... (remaining 24944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 9948 17.59 - 35.19: 1043 35.19 - 52.78: 182 52.78 - 70.37: 28 70.37 - 87.96: 9 Dihedral angle restraints: 11210 sinusoidal: 4090 harmonic: 7120 Sorted by residual: dihedral pdb=" CA VAL L 40 " pdb=" C VAL L 40 " pdb=" N PRO L 41 " pdb=" CA PRO L 41 " ideal model delta harmonic sigma weight residual -180.00 -117.85 -62.15 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA MET P 274 " pdb=" C MET P 274 " pdb=" N ASN P 275 " pdb=" CA ASN P 275 " ideal model delta harmonic sigma weight residual -180.00 -144.70 -35.30 0 5.00e+00 4.00e-02 4.99e+01 dihedral pdb=" CA ALA I 638 " pdb=" C ALA I 638 " pdb=" N LEU I 639 " pdb=" CA LEU I 639 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 11207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2340 0.052 - 0.103: 521 0.103 - 0.155: 139 0.155 - 0.206: 18 0.206 - 0.258: 10 Chirality restraints: 3028 Sorted by residual: chirality pdb=" CB VAL P 224 " pdb=" CA VAL P 224 " pdb=" CG1 VAL P 224 " pdb=" CG2 VAL P 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU Q 211 " pdb=" CB LEU Q 211 " pdb=" CD1 LEU Q 211 " pdb=" CD2 LEU Q 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO Y 223 " pdb=" N PRO Y 223 " pdb=" C PRO Y 223 " pdb=" CB PRO Y 223 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3025 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 40 " -0.061 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO L 41 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO L 41 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 41 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 40 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C VAL L 40 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL L 40 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO L 41 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 437 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C VAL I 437 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL I 437 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS I 438 " -0.014 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4935 2.81 - 3.33: 16351 3.33 - 3.85: 29096 3.85 - 4.38: 30891 4.38 - 4.90: 55881 Nonbonded interactions: 137154 Sorted by model distance: nonbonded pdb=" O ILE I 383 " pdb=" OG SER I 387 " model vdw 2.282 2.440 nonbonded pdb=" O ILE K 70 " pdb=" OG SER K 73 " model vdw 2.300 2.440 nonbonded pdb=" O LEU I 535 " pdb=" OH TYR I 560 " model vdw 2.304 2.440 nonbonded pdb=" O SER O 214 " pdb=" OG SER O 214 " model vdw 2.311 2.440 nonbonded pdb=" O SER O 153 " pdb=" OG SER O 153 " model vdw 2.319 2.440 ... (remaining 137149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.550 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 46.440 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.005 0.069 18425 Z= 0.290 Angle : 0.840 15.451 24949 Z= 0.454 Chirality : 0.050 0.258 3028 Planarity : 0.006 0.093 3122 Dihedral : 14.608 87.965 6534 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 0.27 % Allowed : 7.68 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -3.18 (0.14), residues: 2278 helix: -1.42 (0.11), residues: 1370 sheet: -2.46 (0.34), residues: 214 loop : -3.11 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 102 HIS 0.006 0.001 HIS I 694 PHE 0.026 0.002 PHE I 610 TYR 0.027 0.002 TYR Z 43 ARG 0.004 0.000 ARG N 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 493 time to evaluate : 2.273 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: H 15 LEU cc_start: 0.8161 (tp) cc_final: 0.7869 (mt) REVERT: H 24 ARG cc_start: 0.6014 (mtp-110) cc_final: 0.5625 (mtm180) REVERT: I 405 TYR cc_start: 0.8752 (m-80) cc_final: 0.8510 (m-80) REVERT: I 438 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7994 (mmtm) REVERT: I 590 ASN cc_start: 0.7613 (t0) cc_final: 0.7315 (t0) REVERT: I 611 PHE cc_start: 0.7081 (m-80) cc_final: 0.6861 (m-80) REVERT: I 697 ARG cc_start: 0.4641 (ptp-170) cc_final: 0.4086 (mmt180) REVERT: K 99 ASP cc_start: 0.7862 (m-30) cc_final: 0.7609 (m-30) REVERT: K 104 LEU cc_start: 0.7341 (tp) cc_final: 0.6814 (tp) REVERT: K 124 GLN cc_start: 0.5331 (tm-30) cc_final: 0.4800 (mm-40) REVERT: L 107 TYR cc_start: 0.6893 (m-80) cc_final: 0.6392 (m-80) REVERT: L 217 MET cc_start: 0.7229 (mtt) cc_final: 0.6997 (mtm) REVERT: N 21 PHE cc_start: 0.7064 (t80) cc_final: 0.6701 (t80) REVERT: N 392 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8134 (tm-30) REVERT: O 184 ILE cc_start: 0.8246 (mp) cc_final: 0.8004 (mp) REVERT: O 280 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7865 (mtmt) REVERT: O 292 LYS cc_start: 0.8021 (mttp) cc_final: 0.7446 (tppt) REVERT: O 313 ILE cc_start: 0.8264 (mp) cc_final: 0.7974 (mt) REVERT: O 341 LYS cc_start: 0.5903 (mttt) cc_final: 0.5656 (mmtm) REVERT: P 173 ASP cc_start: 0.7331 (m-30) cc_final: 0.7084 (m-30) REVERT: P 254 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8333 (ttpp) REVERT: Q 266 GLN cc_start: 0.8324 (tp40) cc_final: 0.8073 (mm-40) REVERT: U 182 SER cc_start: 0.8586 (t) cc_final: 0.8351 (p) REVERT: U 185 MET cc_start: 0.8147 (mmm) cc_final: 0.7944 (tpp) REVERT: U 200 ASN cc_start: 0.7350 (m-40) cc_final: 0.7086 (t0) REVERT: U 241 ASN cc_start: 0.8147 (m-40) cc_final: 0.7928 (m-40) REVERT: Y 15 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7808 (tp30) REVERT: Y 69 ASN cc_start: 0.8479 (m-40) cc_final: 0.8192 (t0) REVERT: Z 62 LYS cc_start: 0.8914 (tttt) cc_final: 0.8205 (mtmt) REVERT: Z 71 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7827 (ttp80) REVERT: Z 80 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8509 (tp-100) outliers start: 5 outliers final: 1 residues processed: 498 average time/residue: 0.3575 time to fit residues: 252.6955 Evaluate side-chains 321 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 215 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.0470 chunk 180 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 GLN I 467 GLN I 490 GLN I 521 GLN I 595 ASN ** I 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN K 122 GLN L 36 GLN L 118 GLN L 213 HIS L 238 GLN N 141 HIS N 165 ASN N 213 HIS ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 238 HIS O 247 GLN O 274 GLN O 322 ASN P 135 GLN P 297 GLN Q 245 GLN U 219 GLN U 228 GLN Y 170 GLN Y 198 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18425 Z= 0.172 Angle : 0.570 9.110 24949 Z= 0.295 Chirality : 0.039 0.237 3028 Planarity : 0.004 0.085 3122 Dihedral : 4.662 45.839 2543 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.98 % Allowed : 15.48 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2278 helix: 0.80 (0.13), residues: 1407 sheet: -2.09 (0.33), residues: 225 loop : -2.76 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.003 0.001 HIS N 149 PHE 0.052 0.002 PHE I 546 TYR 0.030 0.001 TYR Z 43 ARG 0.008 0.001 ARG P 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 353 time to evaluate : 2.006 Fit side-chains revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6201 (mtp-110) cc_final: 0.5854 (mtm180) REVERT: H 50 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7455 (tp-100) REVERT: I 424 TRP cc_start: 0.8482 (t60) cc_final: 0.8200 (t60) REVERT: I 438 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7905 (mmtm) REVERT: I 489 MET cc_start: 0.7874 (mmp) cc_final: 0.7402 (mmp) REVERT: I 497 LYS cc_start: 0.7638 (mttt) cc_final: 0.7267 (tptm) REVERT: I 569 MET cc_start: 0.6193 (ptm) cc_final: 0.5967 (ptp) REVERT: I 590 ASN cc_start: 0.7465 (t0) cc_final: 0.7186 (t0) REVERT: I 697 ARG cc_start: 0.4635 (ptp-170) cc_final: 0.3900 (mmt90) REVERT: K 99 ASP cc_start: 0.7787 (m-30) cc_final: 0.7479 (m-30) REVERT: K 104 LEU cc_start: 0.7142 (tp) cc_final: 0.6915 (tp) REVERT: L 12 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7806 (tttp) REVERT: L 80 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8506 (mttt) REVERT: L 101 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7785 (mm-40) REVERT: L 217 MET cc_start: 0.7533 (mtt) cc_final: 0.7332 (mtm) REVERT: L 238 GLN cc_start: 0.8557 (tp40) cc_final: 0.8326 (tp-100) REVERT: N 21 PHE cc_start: 0.6950 (t80) cc_final: 0.6676 (t80) REVERT: N 97 MET cc_start: 0.7760 (ttm) cc_final: 0.7545 (ttm) REVERT: O 280 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7812 (mtmt) REVERT: O 292 LYS cc_start: 0.7534 (mttp) cc_final: 0.6992 (tppt) REVERT: O 313 ILE cc_start: 0.8394 (mp) cc_final: 0.8071 (mt) REVERT: O 341 LYS cc_start: 0.5964 (mttt) cc_final: 0.5686 (mmtm) REVERT: P 248 ASP cc_start: 0.8148 (t0) cc_final: 0.7925 (t0) REVERT: P 254 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8458 (ttpp) REVERT: P 275 ASN cc_start: 0.6620 (OUTLIER) cc_final: 0.6207 (p0) REVERT: P 347 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Q 266 GLN cc_start: 0.8285 (tp40) cc_final: 0.7982 (mm-40) REVERT: U 182 SER cc_start: 0.8574 (t) cc_final: 0.8337 (p) REVERT: U 200 ASN cc_start: 0.7408 (m-40) cc_final: 0.7144 (t0) REVERT: Y 15 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7716 (tp30) REVERT: Y 69 ASN cc_start: 0.8379 (m-40) cc_final: 0.8109 (t0) REVERT: Y 119 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8085 (ttmm) REVERT: Y 198 ASN cc_start: 0.7732 (t0) cc_final: 0.7278 (t0) REVERT: Z 62 LYS cc_start: 0.8967 (tttt) cc_final: 0.8263 (mtmt) REVERT: Z 71 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7752 (ttp80) outliers start: 36 outliers final: 15 residues processed: 376 average time/residue: 0.3203 time to fit residues: 176.7038 Evaluate side-chains 323 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 306 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain Q residue 379 SER Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN L 96 ASN L 185 ASN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 290 GLN O 274 GLN P 135 GLN P 297 GLN ** U 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18425 Z= 0.191 Angle : 0.551 8.670 24949 Z= 0.286 Chirality : 0.039 0.269 3028 Planarity : 0.004 0.080 3122 Dihedral : 4.434 45.900 2543 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.47 % Allowed : 18.22 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2278 helix: 1.61 (0.14), residues: 1408 sheet: -1.77 (0.34), residues: 225 loop : -2.56 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.002 0.001 HIS N 149 PHE 0.020 0.001 PHE I 610 TYR 0.028 0.002 TYR Z 43 ARG 0.006 0.000 ARG L 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 305 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6200 (mtp-110) cc_final: 0.5832 (mtm180) REVERT: I 424 TRP cc_start: 0.8503 (t60) cc_final: 0.8231 (t60) REVERT: I 438 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7918 (mmtm) REVERT: I 440 MET cc_start: 0.9102 (mmm) cc_final: 0.8874 (mmm) REVERT: I 489 MET cc_start: 0.7990 (mmp) cc_final: 0.7444 (mmp) REVERT: I 542 MET cc_start: 0.6497 (tpp) cc_final: 0.6188 (tpp) REVERT: I 569 MET cc_start: 0.6288 (ptm) cc_final: 0.6047 (ptp) REVERT: I 590 ASN cc_start: 0.7484 (t0) cc_final: 0.7213 (t0) REVERT: I 697 ARG cc_start: 0.4585 (ptp-170) cc_final: 0.4293 (mmm-85) REVERT: K 99 ASP cc_start: 0.7802 (m-30) cc_final: 0.7476 (m-30) REVERT: L 79 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.7861 (p) REVERT: L 80 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8620 (mttt) REVERT: N 21 PHE cc_start: 0.6857 (t80) cc_final: 0.6493 (t80) REVERT: N 255 MET cc_start: 0.9048 (mmm) cc_final: 0.8775 (mmm) REVERT: O 280 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7804 (mtmt) REVERT: O 346 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8056 (mm) REVERT: O 349 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (tt) REVERT: P 248 ASP cc_start: 0.8129 (t0) cc_final: 0.7916 (t0) REVERT: P 254 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8499 (ttpp) REVERT: P 347 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8175 (tm-30) REVERT: Q 266 GLN cc_start: 0.8258 (tp40) cc_final: 0.7961 (mm-40) REVERT: U 182 SER cc_start: 0.8567 (t) cc_final: 0.8356 (p) REVERT: U 200 ASN cc_start: 0.7457 (m-40) cc_final: 0.7152 (t0) REVERT: Y 15 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7645 (tp30) REVERT: Y 69 ASN cc_start: 0.8403 (m-40) cc_final: 0.8091 (t0) REVERT: Y 119 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8124 (ttmm) REVERT: Y 198 ASN cc_start: 0.7851 (t0) cc_final: 0.7435 (t0) REVERT: Z 4 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7272 (tm-30) REVERT: Z 8 HIS cc_start: 0.7578 (t-90) cc_final: 0.7311 (m-70) REVERT: Z 17 THR cc_start: 0.7820 (p) cc_final: 0.7568 (t) REVERT: Z 62 LYS cc_start: 0.8925 (tttt) cc_final: 0.8245 (mtmt) REVERT: Z 71 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7722 (ttp80) outliers start: 45 outliers final: 24 residues processed: 338 average time/residue: 0.3266 time to fit residues: 162.5115 Evaluate side-chains 313 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 286 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 297 GLN Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 89 THR Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 ASN P 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18425 Z= 0.197 Angle : 0.543 8.659 24949 Z= 0.282 Chirality : 0.040 0.286 3028 Planarity : 0.004 0.074 3122 Dihedral : 4.308 44.088 2543 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.36 % Allowed : 19.70 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2278 helix: 1.97 (0.14), residues: 1412 sheet: -1.56 (0.34), residues: 228 loop : -2.52 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.005 0.001 HIS H 57 PHE 0.019 0.001 PHE I 610 TYR 0.023 0.001 TYR Z 43 ARG 0.008 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 303 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6197 (mtp-110) cc_final: 0.5864 (mtm180) REVERT: I 345 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7106 (tt) REVERT: I 424 TRP cc_start: 0.8541 (t60) cc_final: 0.8239 (t60) REVERT: I 438 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7881 (mmtm) REVERT: I 489 MET cc_start: 0.8077 (mmp) cc_final: 0.7259 (mmt) REVERT: I 542 MET cc_start: 0.6440 (tpp) cc_final: 0.6103 (tpp) REVERT: I 569 MET cc_start: 0.6405 (ptm) cc_final: 0.6195 (ptp) REVERT: I 590 ASN cc_start: 0.7546 (t0) cc_final: 0.7241 (t0) REVERT: I 697 ARG cc_start: 0.4627 (ptp-170) cc_final: 0.4289 (mmm-85) REVERT: K 99 ASP cc_start: 0.7794 (m-30) cc_final: 0.7447 (m-30) REVERT: L 80 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8573 (mttt) REVERT: L 85 MET cc_start: 0.8187 (ttm) cc_final: 0.7927 (ttm) REVERT: L 238 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8253 (tp-100) REVERT: N 21 PHE cc_start: 0.6952 (t80) cc_final: 0.6672 (t80) REVERT: O 280 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7938 (mtmt) REVERT: O 346 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7948 (mm) REVERT: O 349 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (tt) REVERT: P 248 ASP cc_start: 0.8142 (t0) cc_final: 0.7930 (t0) REVERT: P 254 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8503 (tttp) REVERT: Q 266 GLN cc_start: 0.8268 (tp40) cc_final: 0.7778 (tt0) REVERT: Q 335 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7398 (mpp) REVERT: U 182 SER cc_start: 0.8564 (t) cc_final: 0.8355 (p) REVERT: U 200 ASN cc_start: 0.7483 (m-40) cc_final: 0.7162 (t0) REVERT: Y 15 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7643 (tp30) REVERT: Y 69 ASN cc_start: 0.8424 (m-40) cc_final: 0.8086 (t0) REVERT: Y 119 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8222 (ttmm) REVERT: Y 183 GLU cc_start: 0.7041 (tt0) cc_final: 0.6656 (tt0) REVERT: Y 198 ASN cc_start: 0.7705 (t0) cc_final: 0.7356 (t0) REVERT: Z 4 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7221 (tm-30) REVERT: Z 8 HIS cc_start: 0.7604 (t-90) cc_final: 0.7324 (m-70) REVERT: Z 57 LEU cc_start: 0.8873 (tp) cc_final: 0.8599 (tt) REVERT: Z 62 LYS cc_start: 0.8927 (tttt) cc_final: 0.8244 (mtmt) REVERT: Z 71 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7654 (ttp80) outliers start: 43 outliers final: 24 residues processed: 335 average time/residue: 0.3244 time to fit residues: 159.9572 Evaluate side-chains 309 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain Q residue 379 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 171 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18425 Z= 0.177 Angle : 0.533 8.114 24949 Z= 0.276 Chirality : 0.039 0.222 3028 Planarity : 0.003 0.072 3122 Dihedral : 4.179 42.295 2543 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.52 % Allowed : 20.25 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2278 helix: 2.25 (0.14), residues: 1412 sheet: -1.36 (0.35), residues: 228 loop : -2.40 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.003 0.001 HIS N 141 PHE 0.018 0.001 PHE I 610 TYR 0.018 0.001 TYR Y 193 ARG 0.007 0.000 ARG N 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6155 (mtp-110) cc_final: 0.5858 (mtm-85) REVERT: H 125 MET cc_start: 0.6648 (tpp) cc_final: 0.6088 (tpp) REVERT: I 345 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7048 (tt) REVERT: I 424 TRP cc_start: 0.8519 (t60) cc_final: 0.8246 (t60) REVERT: I 438 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7856 (mmtm) REVERT: I 489 MET cc_start: 0.8132 (mmp) cc_final: 0.7468 (mmt) REVERT: I 542 MET cc_start: 0.6448 (tpp) cc_final: 0.6169 (tpp) REVERT: I 569 MET cc_start: 0.6490 (ptm) cc_final: 0.6260 (ptp) REVERT: I 590 ASN cc_start: 0.7527 (t0) cc_final: 0.7240 (t0) REVERT: I 697 ARG cc_start: 0.4576 (ptp-170) cc_final: 0.4145 (mmm-85) REVERT: K 99 ASP cc_start: 0.7823 (m-30) cc_final: 0.7487 (m-30) REVERT: L 80 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8669 (mttt) REVERT: L 85 MET cc_start: 0.8258 (ttm) cc_final: 0.7593 (ttm) REVERT: L 233 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7798 (mp) REVERT: N 21 PHE cc_start: 0.7079 (t80) cc_final: 0.6715 (t80) REVERT: O 280 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7797 (mtmt) REVERT: O 349 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8256 (tt) REVERT: P 126 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7759 (mm-30) REVERT: P 248 ASP cc_start: 0.8107 (t0) cc_final: 0.7887 (t0) REVERT: P 254 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8460 (tttp) REVERT: Q 266 GLN cc_start: 0.8231 (tp40) cc_final: 0.7763 (tt0) REVERT: Q 335 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7374 (mpp) REVERT: U 182 SER cc_start: 0.8547 (t) cc_final: 0.8336 (p) REVERT: Y 15 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7602 (tp30) REVERT: Y 69 ASN cc_start: 0.8422 (m-40) cc_final: 0.8085 (t0) REVERT: Y 119 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8219 (ttmm) REVERT: Y 183 GLU cc_start: 0.7260 (tt0) cc_final: 0.6864 (tt0) REVERT: Y 198 ASN cc_start: 0.7723 (t0) cc_final: 0.7415 (t0) REVERT: Z 4 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7324 (tm-30) REVERT: Z 8 HIS cc_start: 0.7616 (t-90) cc_final: 0.7325 (m-70) REVERT: Z 62 LYS cc_start: 0.8923 (tttt) cc_final: 0.8238 (mtmt) REVERT: Z 71 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7644 (ttp80) REVERT: Z 118 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8535 (tt0) outliers start: 46 outliers final: 29 residues processed: 341 average time/residue: 0.3145 time to fit residues: 158.0078 Evaluate side-chains 314 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain Q residue 379 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 76 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN ** L 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 GLN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18425 Z= 0.169 Angle : 0.534 9.382 24949 Z= 0.274 Chirality : 0.039 0.210 3028 Planarity : 0.004 0.069 3122 Dihedral : 4.096 40.819 2543 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.80 % Allowed : 20.91 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.18 (0.19), residues: 2278 helix: 2.37 (0.14), residues: 1414 sheet: -1.22 (0.35), residues: 228 loop : -2.27 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.005 0.001 HIS Q 382 PHE 0.017 0.001 PHE I 610 TYR 0.016 0.001 TYR Y 193 ARG 0.008 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 300 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6208 (mtp-110) cc_final: 0.5888 (mtm-85) REVERT: I 345 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7004 (tt) REVERT: I 438 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7848 (mmtm) REVERT: I 489 MET cc_start: 0.8152 (mmp) cc_final: 0.7287 (mmt) REVERT: I 542 MET cc_start: 0.6338 (tpp) cc_final: 0.6076 (tpp) REVERT: I 569 MET cc_start: 0.6586 (ptm) cc_final: 0.6366 (ptp) REVERT: I 590 ASN cc_start: 0.7556 (t0) cc_final: 0.7263 (t0) REVERT: I 697 ARG cc_start: 0.4519 (ptp-170) cc_final: 0.4147 (mmm-85) REVERT: K 99 ASP cc_start: 0.7914 (m-30) cc_final: 0.7588 (m-30) REVERT: L 80 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8734 (mttt) REVERT: L 85 MET cc_start: 0.8273 (ttm) cc_final: 0.7751 (ttm) REVERT: L 233 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7764 (mp) REVERT: N 21 PHE cc_start: 0.7154 (t80) cc_final: 0.6778 (t80) REVERT: O 280 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7805 (mtmt) REVERT: O 301 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8617 (mp) REVERT: O 349 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8317 (tt) REVERT: P 126 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7806 (mm-30) REVERT: P 248 ASP cc_start: 0.8117 (t0) cc_final: 0.7889 (t0) REVERT: P 254 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8473 (tttp) REVERT: P 259 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7998 (tp-100) REVERT: Q 266 GLN cc_start: 0.8243 (tp40) cc_final: 0.7784 (tt0) REVERT: Q 335 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7264 (mpp) REVERT: U 182 SER cc_start: 0.8549 (t) cc_final: 0.8337 (p) REVERT: Y 15 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7587 (tp30) REVERT: Y 69 ASN cc_start: 0.8416 (m-40) cc_final: 0.8080 (t0) REVERT: Y 183 GLU cc_start: 0.7294 (tt0) cc_final: 0.6899 (tt0) REVERT: Z 4 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7270 (tm-30) REVERT: Z 62 LYS cc_start: 0.8919 (tttt) cc_final: 0.8235 (mtmt) REVERT: Z 71 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7565 (ttp80) outliers start: 51 outliers final: 31 residues processed: 334 average time/residue: 0.3474 time to fit residues: 171.6707 Evaluate side-chains 313 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 277 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 297 GLN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain Q residue 379 SER Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 193 optimal weight: 0.5980 chunk 128 optimal weight: 0.4980 chunk 229 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 ASN ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18425 Z= 0.155 Angle : 0.538 9.955 24949 Z= 0.275 Chirality : 0.039 0.206 3028 Planarity : 0.003 0.066 3122 Dihedral : 4.003 38.779 2543 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.47 % Allowed : 21.79 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.34 (0.19), residues: 2278 helix: 2.49 (0.14), residues: 1415 sheet: -1.06 (0.35), residues: 228 loop : -2.24 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.003 0.001 HIS Q 382 PHE 0.017 0.001 PHE I 610 TYR 0.014 0.001 TYR P 272 ARG 0.007 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 301 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6162 (mtp-110) cc_final: 0.5848 (mtm-85) REVERT: I 345 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7080 (tt) REVERT: I 438 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7798 (mmtm) REVERT: I 542 MET cc_start: 0.6254 (tpp) cc_final: 0.5998 (tpp) REVERT: I 697 ARG cc_start: 0.4494 (ptp-170) cc_final: 0.4058 (mmt180) REVERT: L 80 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8752 (mttt) REVERT: L 85 MET cc_start: 0.8301 (ttm) cc_final: 0.7730 (ttm) REVERT: L 181 MET cc_start: 0.7752 (tpp) cc_final: 0.7496 (tpp) REVERT: L 233 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7718 (mp) REVERT: N 21 PHE cc_start: 0.7131 (t80) cc_final: 0.6768 (t80) REVERT: O 280 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7794 (mtmt) REVERT: O 349 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8285 (tt) REVERT: P 126 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7795 (mm-30) REVERT: P 248 ASP cc_start: 0.8118 (t0) cc_final: 0.7878 (t0) REVERT: P 259 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7940 (tp40) REVERT: Q 266 GLN cc_start: 0.8221 (tp40) cc_final: 0.7763 (tt0) REVERT: U 182 SER cc_start: 0.8517 (t) cc_final: 0.8297 (p) REVERT: Y 15 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7621 (tp30) REVERT: Y 69 ASN cc_start: 0.8437 (m-40) cc_final: 0.8092 (t0) REVERT: Y 183 GLU cc_start: 0.7276 (tt0) cc_final: 0.6976 (tt0) REVERT: Y 198 ASN cc_start: 0.7582 (t0) cc_final: 0.7287 (t0) REVERT: Z 8 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7335 (m-70) REVERT: Z 57 LEU cc_start: 0.8901 (tp) cc_final: 0.8678 (tt) REVERT: Z 58 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: Z 62 LYS cc_start: 0.8925 (tttt) cc_final: 0.8241 (mtmt) REVERT: Z 71 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7627 (ttp80) REVERT: Z 118 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8534 (tt0) outliers start: 45 outliers final: 28 residues processed: 329 average time/residue: 0.3269 time to fit residues: 157.3379 Evaluate side-chains 316 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 283 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 58 GLU Chi-restraints excluded: chain Z residue 89 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 137 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 180 optimal weight: 0.0020 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 208 GLN ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18425 Z= 0.143 Angle : 0.545 9.481 24949 Z= 0.277 Chirality : 0.038 0.201 3028 Planarity : 0.003 0.063 3122 Dihedral : 3.903 37.073 2543 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.52 % Allowed : 22.39 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.53 (0.19), residues: 2278 helix: 2.62 (0.14), residues: 1415 sheet: -0.86 (0.36), residues: 229 loop : -2.16 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 236 HIS 0.003 0.000 HIS Q 382 PHE 0.016 0.001 PHE I 610 TYR 0.013 0.001 TYR P 272 ARG 0.007 0.000 ARG L 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 311 time to evaluate : 1.979 Fit side-chains revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6196 (mtp-110) cc_final: 0.5859 (mtm-85) REVERT: I 345 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7051 (tt) REVERT: I 438 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7726 (mmtm) REVERT: I 489 MET cc_start: 0.8077 (mmp) cc_final: 0.7541 (mmp) REVERT: I 542 MET cc_start: 0.6251 (tpp) cc_final: 0.5884 (tpp) REVERT: I 546 PHE cc_start: 0.6879 (m-10) cc_final: 0.6031 (m-80) REVERT: I 697 ARG cc_start: 0.4443 (ptp-170) cc_final: 0.4115 (mmm-85) REVERT: K 99 ASP cc_start: 0.7868 (m-30) cc_final: 0.7574 (m-30) REVERT: L 79 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7895 (p) REVERT: L 85 MET cc_start: 0.8326 (ttm) cc_final: 0.7788 (ttm) REVERT: L 181 MET cc_start: 0.7735 (tpp) cc_final: 0.7479 (tpp) REVERT: L 233 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7638 (mp) REVERT: N 21 PHE cc_start: 0.7110 (t80) cc_final: 0.6765 (t80) REVERT: O 280 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7773 (mtmt) REVERT: O 301 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8642 (mp) REVERT: O 349 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8338 (tt) REVERT: P 126 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7794 (mm-30) REVERT: P 248 ASP cc_start: 0.8124 (t0) cc_final: 0.7895 (t0) REVERT: P 259 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7948 (tp40) REVERT: Q 266 GLN cc_start: 0.8213 (tp40) cc_final: 0.7771 (tt0) REVERT: Q 277 MET cc_start: 0.8345 (mmm) cc_final: 0.8024 (mmm) REVERT: U 182 SER cc_start: 0.8507 (t) cc_final: 0.8284 (p) REVERT: U 255 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7730 (mtt180) REVERT: Y 15 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7542 (tp30) REVERT: Y 69 ASN cc_start: 0.8415 (m-40) cc_final: 0.8098 (t0) REVERT: Y 183 GLU cc_start: 0.7293 (tt0) cc_final: 0.6984 (tt0) REVERT: Z 8 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7628 (m-70) REVERT: Z 57 LEU cc_start: 0.8900 (tp) cc_final: 0.8676 (tt) REVERT: Z 62 LYS cc_start: 0.8926 (tttt) cc_final: 0.8250 (mtmt) REVERT: Z 118 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8556 (tt0) outliers start: 46 outliers final: 30 residues processed: 340 average time/residue: 0.3200 time to fit residues: 159.7332 Evaluate side-chains 325 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 289 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 184 GLN U 208 GLN ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18425 Z= 0.313 Angle : 0.652 11.062 24949 Z= 0.332 Chirality : 0.042 0.248 3028 Planarity : 0.004 0.065 3122 Dihedral : 4.281 38.785 2543 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.47 % Allowed : 23.38 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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 (0.19), residues: 2278 helix: 2.34 (0.14), residues: 1417 sheet: -0.96 (0.36), residues: 234 loop : -2.28 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 102 HIS 0.004 0.001 HIS N 213 PHE 0.025 0.002 PHE O 178 TYR 0.018 0.002 TYR Y 193 ARG 0.009 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: H 24 ARG cc_start: 0.6313 (mtp-110) cc_final: 0.5932 (mtm-85) REVERT: I 345 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7168 (tt) REVERT: I 438 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7868 (mmtm) REVERT: I 489 MET cc_start: 0.8112 (mmp) cc_final: 0.7751 (mmt) REVERT: I 542 MET cc_start: 0.6353 (tpp) cc_final: 0.5776 (tpp) REVERT: I 546 PHE cc_start: 0.6915 (m-10) cc_final: 0.6061 (m-80) REVERT: I 697 ARG cc_start: 0.4501 (ptp-170) cc_final: 0.3535 (mmt90) REVERT: K 99 ASP cc_start: 0.7886 (m-30) cc_final: 0.7560 (m-30) REVERT: L 85 MET cc_start: 0.8276 (ttm) cc_final: 0.8050 (ttm) REVERT: L 233 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7807 (mp) REVERT: N 21 PHE cc_start: 0.7204 (t80) cc_final: 0.6864 (t80) REVERT: O 280 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7944 (mtmt) REVERT: O 301 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8719 (mp) REVERT: O 349 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (tt) REVERT: P 126 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7786 (mm-30) REVERT: P 219 ARG cc_start: 0.7512 (ttp-110) cc_final: 0.7214 (ptm160) REVERT: P 248 ASP cc_start: 0.8188 (t0) cc_final: 0.7927 (t0) REVERT: Q 266 GLN cc_start: 0.8290 (tp40) cc_final: 0.7806 (tt0) REVERT: Q 277 MET cc_start: 0.8342 (mmm) cc_final: 0.8106 (mmm) REVERT: U 182 SER cc_start: 0.8565 (t) cc_final: 0.8300 (p) REVERT: U 253 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7424 (m-40) REVERT: Y 15 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7634 (tp30) REVERT: Y 119 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8308 (ttmm) REVERT: Y 183 GLU cc_start: 0.7409 (tt0) cc_final: 0.7117 (tt0) REVERT: Z 8 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7713 (m-70) REVERT: Z 62 LYS cc_start: 0.8871 (tttt) cc_final: 0.8261 (mtmt) REVERT: Z 96 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8425 (mppt) REVERT: Z 118 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8569 (tt0) outliers start: 45 outliers final: 33 residues processed: 328 average time/residue: 0.3356 time to fit residues: 162.6791 Evaluate side-chains 326 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 287 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain I residue 724 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 254 LYS Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS I 590 ASN ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18425 Z= 0.221 Angle : 0.606 12.034 24949 Z= 0.308 Chirality : 0.040 0.218 3028 Planarity : 0.004 0.062 3122 Dihedral : 4.132 37.014 2543 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.31 % Allowed : 23.93 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.36 (0.19), residues: 2278 helix: 2.48 (0.14), residues: 1414 sheet: -0.97 (0.36), residues: 228 loop : -2.20 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 102 HIS 0.002 0.001 HIS N 213 PHE 0.017 0.001 PHE O 178 TYR 0.018 0.001 TYR L 177 ARG 0.006 0.000 ARG N 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 293 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 9 TRP cc_start: 0.5550 (t-100) cc_final: 0.5207 (m-10) REVERT: H 24 ARG cc_start: 0.6338 (mtp-110) cc_final: 0.5889 (mtm-85) REVERT: I 345 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7077 (tt) REVERT: I 438 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7766 (mmtm) REVERT: I 489 MET cc_start: 0.8228 (mmp) cc_final: 0.7744 (mmp) REVERT: I 542 MET cc_start: 0.6278 (tpp) cc_final: 0.5883 (tpp) REVERT: I 546 PHE cc_start: 0.6879 (m-10) cc_final: 0.6041 (m-80) REVERT: I 569 MET cc_start: 0.6605 (ptp) cc_final: 0.6079 (ptp) REVERT: I 697 ARG cc_start: 0.4427 (ptp-170) cc_final: 0.3492 (mmt90) REVERT: K 99 ASP cc_start: 0.7854 (m-30) cc_final: 0.7550 (m-30) REVERT: L 181 MET cc_start: 0.7763 (tpp) cc_final: 0.7502 (tpp) REVERT: L 233 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7729 (mp) REVERT: N 21 PHE cc_start: 0.7101 (t80) cc_final: 0.6532 (t80) REVERT: N 25 MET cc_start: 0.7527 (mmm) cc_final: 0.7170 (mmp) REVERT: O 185 ASP cc_start: 0.8414 (p0) cc_final: 0.8205 (p0) REVERT: O 280 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7796 (mtmt) REVERT: O 301 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8623 (mp) REVERT: O 349 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8339 (tt) REVERT: P 126 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7771 (mm-30) REVERT: P 219 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7227 (ptm160) REVERT: P 248 ASP cc_start: 0.8114 (t0) cc_final: 0.7862 (t0) REVERT: Q 266 GLN cc_start: 0.8236 (tp40) cc_final: 0.7787 (tt0) REVERT: Q 277 MET cc_start: 0.8366 (mmm) cc_final: 0.8099 (mmm) REVERT: U 182 SER cc_start: 0.8549 (t) cc_final: 0.8309 (p) REVERT: U 253 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7425 (m-40) REVERT: Y 15 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7615 (tp30) REVERT: Y 183 GLU cc_start: 0.7433 (tt0) cc_final: 0.7127 (tt0) REVERT: Z 8 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7995 (m-70) REVERT: Z 62 LYS cc_start: 0.8867 (tttt) cc_final: 0.8303 (mtmt) REVERT: Z 96 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8441 (mppt) REVERT: Z 118 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8569 (tt0) outliers start: 42 outliers final: 32 residues processed: 324 average time/residue: 0.3318 time to fit residues: 158.9446 Evaluate side-chains 325 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 287 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 590 ASN ** I 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133322 restraints weight = 26940.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129619 restraints weight = 43567.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127998 restraints weight = 33162.190| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18425 Z= 0.288 Angle : 0.641 11.359 24949 Z= 0.326 Chirality : 0.042 0.227 3028 Planarity : 0.004 0.063 3122 Dihedral : 4.237 37.068 2543 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.47 % Allowed : 23.66 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2278 helix: 2.38 (0.14), residues: 1419 sheet: -0.99 (0.36), residues: 227 loop : -2.28 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 102 HIS 0.003 0.001 HIS N 213 PHE 0.021 0.002 PHE O 178 TYR 0.019 0.001 TYR Y 193 ARG 0.007 0.001 ARG N 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3881.06 seconds wall clock time: 70 minutes 57.94 seconds (4257.94 seconds total)