Starting phenix.real_space_refine on Sat Feb 17 09:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue8_20750/02_2024/6ue8_20750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue8_20750/02_2024/6ue8_20750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue8_20750/02_2024/6ue8_20750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue8_20750/02_2024/6ue8_20750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue8_20750/02_2024/6ue8_20750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue8_20750/02_2024/6ue8_20750.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.012 sd= 0.434 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 11463 2.51 5 N 3144 2.21 5 O 3478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "F PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 357": "OE1" <-> "OE2" Residue "K TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 18183 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1686 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4130 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1656 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1666 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1570 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1556 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 103 Chain: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1581 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1543 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.26, per 1000 atoms: 0.56 Number of scatterers: 18183 At special positions: 0 Unit cell: (173.196, 147.726, 180.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3478 8.00 N 3144 7.00 C 11463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.02 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.03 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 471 " - pdb=" SG CYS E 471 " distance=2.02 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS H 299 " distance=2.04 Simple disulfide: pdb=" SG CYS E 299 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 369 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 323 " distance=2.03 Simple disulfide: pdb=" SG CYS H 369 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 242 " - pdb=" SG CYS L 299 " distance=2.04 Simple disulfide: pdb=" SG CYS K 266 " - pdb=" SG CYS K 323 " distance=2.04 Simple disulfide: pdb=" SG CYS K 299 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 369 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 266 " - pdb=" SG CYS L 323 " distance=2.03 Simple disulfide: pdb=" SG CYS L 369 " - pdb=" SG CYS L 432 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 337 " " NAG B 501 " - " ASN B 337 " " NAG C 603 " - " ASN C 65 " " NAG F 501 " - " ASN F 337 " " NAG G 501 " - " ASN G 337 " " NAG I 1 " - " ASN C 72 " " NAG J 1 " - " ASN D 49 " Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 53 sheets defined 10.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.606A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.672A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.537A pdb=" N LYS A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.953A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 4.205A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 362' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.681A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.849A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 276 " --> pdb=" O PRO C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.596A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.690A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.717A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 removed outlier: 4.292A pdb=" N ASP C 520 " --> pdb=" O THR C 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 312 through 318 removed outlier: 4.175A pdb=" N ASN F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 3.730A pdb=" N LEU F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 360' Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.895A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 355 through 360 removed outlier: 3.679A pdb=" N LEU G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 360' Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.709A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.628A pdb=" N TRP E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 362 removed outlier: 4.439A pdb=" N LEU E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 357 through 362' Processing helix chain 'E' and resid 391 through 395 removed outlier: 4.264A pdb=" N TYR E 395 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.850A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 311 through 316 removed outlier: 3.522A pdb=" N TRP H 315 " --> pdb=" O CYS H 311 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 311 through 316' Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.716A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN H 362 " --> pdb=" O GLU H 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 357 through 362' Processing helix chain 'H' and resid 391 through 395 removed outlier: 4.133A pdb=" N TYR H 395 " --> pdb=" O ARG H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 312 through 318 removed outlier: 3.610A pdb=" N GLY K 318 " --> pdb=" O PRO K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 362 removed outlier: 3.652A pdb=" N LEU K 361 " --> pdb=" O GLU K 357 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN K 362 " --> pdb=" O GLU K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 427 removed outlier: 3.905A pdb=" N TRP K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 256 removed outlier: 3.869A pdb=" N ASP L 255 " --> pdb=" O ALA L 252 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU L 256 " --> pdb=" O LEU L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 252 through 256' Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.884A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.620A pdb=" N SER A 247 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 267 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 290 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.540A pdb=" N ALA A 336 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.907A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.907A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR A 410 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 63 removed outlier: 8.198A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR D 63 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 463 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE K 458 " --> pdb=" O HIS L 457 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL K 460 " --> pdb=" O ASN L 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.754A pdb=" N ARG B 245 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY B 270 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 281 removed outlier: 3.595A pdb=" N PHE B 321 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 338 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.812A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.812A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.269A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.749A pdb=" N ASN C 65 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 125 removed outlier: 7.068A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.569A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 149 through 151 removed outlier: 3.580A pdb=" N LYS C 149 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 151 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR C 154 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 3.565A pdb=" N GLU C 225 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.642A pdb=" N VAL C 292 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 343 removed outlier: 3.527A pdb=" N GLY C 343 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 348 through 354 removed outlier: 3.607A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 351 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 408 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 460 through 462 removed outlier: 4.015A pdb=" N LEU C 460 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 513 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 511 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 484 through 487 removed outlier: 3.950A pdb=" N GLN C 486 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 479 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 533 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 11 removed outlier: 6.772A pdb=" N ILE D 18 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 10 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA D 16 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 33 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 34 " --> pdb=" O HIS F 457 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASN F 459 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG D 36 " --> pdb=" O ASN F 459 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER F 461 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 38 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL F 463 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 40 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA F 465 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 42 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 458 " --> pdb=" O ASN H 459 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER H 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 460 " --> pdb=" O SER H 461 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL H 463 " --> pdb=" O VAL G 460 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL G 462 " --> pdb=" O VAL H 463 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 78 Processing sheet with id=AC7, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AC8, first strand: chain 'F' and resid 245 through 247 removed outlier: 3.526A pdb=" N CYS F 266 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 268 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 304 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 279 through 280 removed outlier: 3.661A pdb=" N ALA F 325 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 334 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.804A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.804A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'G' and resid 322 through 323 Processing sheet with id=AD5, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.016A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.016A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD8, first strand: chain 'E' and resid 245 through 249 Processing sheet with id=AD9, first strand: chain 'E' and resid 295 through 297 removed outlier: 3.678A pdb=" N SER E 303 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP E 297 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.381A pdb=" N THR E 368 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.381A pdb=" N THR E 368 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 412 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 401 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 388 through 389 removed outlier: 3.737A pdb=" N GLN E 388 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 385 " --> pdb=" O GLN E 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 380 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 384 " --> pdb=" O SER E 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 245 through 249 removed outlier: 3.522A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER H 247 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 267 " --> pdb=" O SER H 247 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS H 249 " --> pdb=" O THR H 265 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR H 265 " --> pdb=" O HIS H 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 320 through 322 removed outlier: 3.516A pdb=" N PHE H 321 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 348 through 352 removed outlier: 4.135A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 348 through 352 removed outlier: 4.135A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR H 410 " --> pdb=" O GLU H 403 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 388 through 389 removed outlier: 3.685A pdb=" N PHE H 430 " --> pdb=" O ILE H 448 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 247 through 248 removed outlier: 4.487A pdb=" N SER K 247 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR K 267 " --> pdb=" O SER K 247 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU K 268 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL K 304 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 247 through 248 removed outlier: 4.487A pdb=" N SER K 247 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR K 267 " --> pdb=" O SER K 247 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU K 268 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL K 304 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.501A pdb=" N LEU K 334 " --> pdb=" O ALA K 325 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.058A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.058A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.958A pdb=" N PHE K 430 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 448 " --> pdb=" O PHE K 430 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 350 through 351 removed outlier: 3.723A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 350 through 351 removed outlier: 3.723A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 388 through 389 removed outlier: 4.111A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU L 380 " --> pdb=" O GLY L 435 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 435 " --> pdb=" O LEU L 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1398 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: 6.23 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5827 1.34 - 1.46: 4438 1.46 - 1.59: 8234 1.59 - 1.72: 0 1.72 - 1.84: 115 Bond restraints: 18614 Sorted by residual: bond pdb=" C GLU K 389 " pdb=" N LEU K 390 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 8.79e+00 bond pdb=" C GLU A 389 " pdb=" N LEU A 390 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.21e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N LEU G 359 " pdb=" CA LEU G 359 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.11e+00 bond pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.89e+00 ... (remaining 18609 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.81: 621 105.81 - 112.92: 10346 112.92 - 120.03: 6006 120.03 - 127.15: 8236 127.15 - 134.26: 318 Bond angle restraints: 25527 Sorted by residual: angle pdb=" C ALA L 438 " pdb=" N LEU L 439 " pdb=" CA LEU L 439 " ideal model delta sigma weight residual 120.68 131.71 -11.03 1.52e+00 4.33e-01 5.27e+01 angle pdb=" C HIS E 249 " pdb=" N ARG E 250 " pdb=" CA ARG E 250 " ideal model delta sigma weight residual 121.03 131.25 -10.22 1.60e+00 3.91e-01 4.08e+01 angle pdb=" C VAL E 307 " pdb=" N LEU E 308 " pdb=" CA LEU E 308 " ideal model delta sigma weight residual 122.65 132.54 -9.89 1.66e+00 3.63e-01 3.55e+01 angle pdb=" N GLY C 527 " pdb=" CA GLY C 527 " pdb=" C GLY C 527 " ideal model delta sigma weight residual 111.42 119.49 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" C TRP L 281 " pdb=" N THR L 282 " pdb=" CA THR L 282 " ideal model delta sigma weight residual 120.26 127.47 -7.21 1.34e+00 5.57e-01 2.89e+01 ... (remaining 25522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 10553 22.23 - 44.46: 646 44.46 - 66.69: 56 66.69 - 88.93: 13 88.93 - 111.16: 13 Dihedral angle restraints: 11281 sinusoidal: 4183 harmonic: 7098 Sorted by residual: dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 323 " pdb=" CB CYS H 323 " ideal model delta sinusoidal sigma weight residual 93.00 164.04 -71.04 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual 93.00 159.61 -66.61 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual -86.00 -149.92 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 11278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2532 0.080 - 0.160: 479 0.160 - 0.239: 49 0.239 - 0.319: 5 0.319 - 0.399: 3 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CG LEU L 264 " pdb=" CB LEU L 264 " pdb=" CD1 LEU L 264 " pdb=" CD2 LEU L 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3065 not shown) Planarity restraints: 3280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 55 " 0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO D 56 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 327 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO G 328 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 282 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO G 283 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 283 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 283 " 0.037 5.00e-02 4.00e+02 ... (remaining 3277 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 707 2.70 - 3.25: 14778 3.25 - 3.80: 25886 3.80 - 4.35: 30411 4.35 - 4.90: 54662 Nonbonded interactions: 126444 Sorted by model distance: nonbonded pdb=" NH2 ARG D 21 " pdb=" OE1 GLU D 35 " model vdw 2.144 2.520 nonbonded pdb=" O LEU C 460 " pdb=" OG1 THR C 512 " model vdw 2.248 2.440 nonbonded pdb=" O SER C 506 " pdb=" OG SER C 506 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.275 2.440 nonbonded pdb=" O LEU L 396 " pdb=" OG SER L 415 " model vdw 2.277 2.440 ... (remaining 126439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 242 through 244 or (resid 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 through 253 or (resid 254 through 255 \ and (name N or name CA or name C or name O or name CB )) or resid 256 through 25 \ 9 or (resid 260 through 262 and (name N or name CA or name C or name O or name C \ B )) or resid 263 through 270 or (resid 271 through 272 and (name N or name CA o \ r name C or name O or name CB )) or resid 276 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 312 or (re \ sid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB )) or resid 342 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 through \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throug \ h 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 through 387 or (resid 388 and (name N or name CA or name C or name O o \ r name CB )) or resid 389 through 391 or (resid 392 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 404 or (resid 405 \ through 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 424 or (resid 425 through 426 and (name N or name CA or name C or name \ O or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C or \ name O or name CB )) or resid 429 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 456 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 295 or (resid 296 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throu \ gh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 356 or (resid 357 through 363 and (name N or name CA or name \ C or name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 3 \ 91 or (resid 392 through 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 404 or (resid 405 through 406 and (name N or name CA \ or name C or name O or name CB )) or resid 407 through 424 or (resid 425 through \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 t \ hrough 445 or (resid 446 and (name N or name CA or name C or name O or name CB ) \ ) or resid 447 through 449 or (resid 450 and (name N or name CA or name C or nam \ e O or name CB )) or resid 456 through 464)) selection = (chain 'E' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 450 o \ r resid 456 through 464)) selection = (chain 'F' and (resid 242 through 259 or (resid 260 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 272 or resid 276 t \ hrough 310 or (resid 311 through 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 340 or (resid 341 and (name N or name CA or n \ ame C or name O or name CB )) or resid 342 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 356 or (resid \ 357 through 363 and (name N or name CA or name C or name O or name CB )) or res \ id 364 through 376 or (resid 377 and (name N or name CA or name C or name O or n \ ame CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 424 or (resid 425 through 426 and (name N or name CA or n \ ame C or name O or name CB )) or resid 427 through 445 or (resid 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 through 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 456 throu \ gh 464)) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 316 or (resid 317 and (name N or name CA or name C or nam \ e O or name CB )) or resid 318 through 340 or (resid 341 and (name N or name CA \ or name C or name O or name CB )) or resid 342 through 345 or (resid 346 and (na \ me N or name CA or name C or name O or name CB )) or resid 347 through 356 or (r \ esid 357 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 4 \ 04 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 424 or (resid 425 through 426 and (na \ me N or name CA or name C or name O or name CB )) or resid 427 through 445 or (r \ esid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 t \ hrough 449 or (resid 450 and (name N or name CA or name C or name O or name CB ) \ ) or resid 456 through 464)) selection = (chain 'H' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 14 through 424 or (resid 425 through 426 and (name N or name CA or name C or nam \ e O or name CB )) or resid 427 through 450 or resid 456 through 464)) selection = (chain 'K' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 340 or (resid 341 and (na \ me N or name CA or name C or name O or name CB )) or resid 342 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 356 or (resid 357 through 363 and (name N or name CA or name C or name O \ or name CB )) or resid 364 through 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 392 or (resid \ 393 through 394 and (name N or name CA or name C or name O or name CB )) or res \ id 395 through 404 or (resid 405 through 406 and (name N or name CA or name C or \ name O or name CB )) or resid 407 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 450 or resid 456 thro \ ugh 464)) selection = (chain 'L' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 345 or (resid 346 and (name N or name CA or name C or nam \ e O or name CB )) or resid 347 through 358 or (resid 359 through 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 376 or (resid \ 377 and (name N or name CA or name C or name O or name CB )) or resid 378 throu \ gh 392 or (resid 393 through 394 and (name N or name CA or name C or name O or n \ ame CB )) or resid 395 through 425 or (resid 426 and (name N or name CA or name \ C or name O or name CB )) or resid 427 through 450 or resid 456 through 464)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.380 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 50.620 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.008 0.083 18614 Z= 0.559 Angle : 1.143 12.081 25527 Z= 0.623 Chirality : 0.062 0.399 3068 Planarity : 0.009 0.085 3273 Dihedral : 14.435 111.156 6576 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 0.48 % Allowed : 9.91 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.18 % 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: -3.88 (0.14), residues: 2437 helix: -4.46 (0.19), residues: 136 sheet: -1.55 (0.17), residues: 783 loop : -3.14 (0.13), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 383 HIS 0.009 0.002 HIS E 436 PHE 0.024 0.003 PHE C 136 TYR 0.024 0.003 TYR A 395 ARG 0.011 0.001 ARG L 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 450 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 ASP cc_start: 0.8127 (p0) cc_final: 0.7844 (p0) REVERT: K 378 ASP cc_start: 0.7088 (m-30) cc_final: 0.6853 (m-30) REVERT: L 411 TYR cc_start: 0.4961 (m-80) cc_final: 0.4398 (m-80) outliers start: 9 outliers final: 1 residues processed: 457 average time/residue: 1.2880 time to fit residues: 654.7752 Evaluate side-chains 242 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 chunk 142 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 291 GLN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS B 343 ASN C 68 ASN C 247 ASN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN G 263 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN E 459 ASN ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN K 385 GLN L 249 HIS L 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18614 Z= 0.215 Angle : 0.782 11.926 25527 Z= 0.385 Chirality : 0.045 0.270 3068 Planarity : 0.007 0.067 3273 Dihedral : 8.647 69.692 2804 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.17 % Allowed : 18.97 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.15), residues: 2437 helix: -3.63 (0.27), residues: 127 sheet: -0.75 (0.18), residues: 788 loop : -2.62 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 281 HIS 0.005 0.001 HIS F 457 PHE 0.017 0.001 PHE L 443 TYR 0.014 0.001 TYR C 148 ARG 0.011 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 287 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 483 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.6974 (t) REVERT: F 346 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7452 (ptt-90) REVERT: E 448 ILE cc_start: 0.5212 (OUTLIER) cc_final: 0.4754 (pp) REVERT: H 403 GLU cc_start: 0.7204 (pt0) cc_final: 0.6826 (pm20) REVERT: K 423 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8365 (p0) REVERT: L 385 GLN cc_start: 0.5845 (OUTLIER) cc_final: 0.5138 (tp40) outliers start: 97 outliers final: 36 residues processed: 352 average time/residue: 1.1562 time to fit residues: 459.7506 Evaluate side-chains 257 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 378 ASP Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 278 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 385 GLN Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 185 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN E 350 HIS H 291 GLN K 249 HIS K 385 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18614 Z= 0.264 Angle : 0.773 11.574 25527 Z= 0.374 Chirality : 0.046 0.316 3068 Planarity : 0.006 0.053 3273 Dihedral : 7.001 56.608 2804 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 5.81 % Allowed : 20.40 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2437 helix: -2.72 (0.34), residues: 142 sheet: -0.39 (0.18), residues: 822 loop : -2.44 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 281 HIS 0.007 0.001 HIS F 457 PHE 0.018 0.002 PHE C 75 TYR 0.013 0.001 TYR B 472 ARG 0.012 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 234 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.8850 (tp) cc_final: 0.8624 (tt) REVERT: C 177 ILE cc_start: 0.2668 (OUTLIER) cc_final: 0.2367 (tp) REVERT: C 459 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.6799 (t) REVERT: C 461 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7960 (mmtt) REVERT: C 483 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.6940 (t) REVERT: F 346 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7463 (ptt-90) REVERT: E 448 ILE cc_start: 0.5501 (OUTLIER) cc_final: 0.4763 (mp) REVERT: H 403 GLU cc_start: 0.7508 (pt0) cc_final: 0.7169 (pm20) REVERT: L 346 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6337 (ttm-80) REVERT: L 367 LEU cc_start: 0.6968 (mm) cc_final: 0.6700 (mt) REVERT: L 382 ARG cc_start: 0.5747 (OUTLIER) cc_final: 0.4443 (mtm180) REVERT: L 433 MET cc_start: 0.5893 (mpm) cc_final: 0.4588 (tmm) outliers start: 109 outliers final: 48 residues processed: 306 average time/residue: 1.2109 time to fit residues: 418.2805 Evaluate side-chains 255 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 346 ARG Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 382 ARG Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN C 68 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS G 436 HIS H 385 GLN K 385 GLN K 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 18614 Z= 0.534 Angle : 0.928 14.228 25527 Z= 0.454 Chirality : 0.050 0.260 3068 Planarity : 0.006 0.061 3273 Dihedral : 7.199 55.078 2804 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 7.41 % Allowed : 22.32 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.16), residues: 2437 helix: -2.13 (0.39), residues: 134 sheet: -0.58 (0.18), residues: 797 loop : -2.48 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 281 HIS 0.010 0.002 HIS E 327 PHE 0.024 0.003 PHE E 279 TYR 0.020 0.002 TYR C 541 ARG 0.008 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 214 time to evaluate : 2.383 Fit side-chains revert: symmetry clash REVERT: B 327 HIS cc_start: 0.6015 (OUTLIER) cc_final: 0.5415 (t70) REVERT: C 46 CYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7133 (t) REVERT: C 177 ILE cc_start: 0.4388 (OUTLIER) cc_final: 0.3648 (tp) REVERT: C 459 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7474 (t) REVERT: C 461 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7940 (mmtm) REVERT: D 70 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9053 (ptpp) REVERT: E 445 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: H 315 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.8042 (t60) REVERT: H 368 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8488 (p) REVERT: K 358 GLU cc_start: 0.7938 (pt0) cc_final: 0.7716 (pt0) REVERT: L 346 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6065 (ttm-80) REVERT: L 367 LEU cc_start: 0.7809 (mm) cc_final: 0.7541 (mt) REVERT: L 382 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5077 (mtm180) REVERT: L 433 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6071 (tmt) outliers start: 139 outliers final: 62 residues processed: 314 average time/residue: 1.2071 time to fit residues: 428.4222 Evaluate side-chains 252 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 179 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 GLN Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 346 ARG Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 382 ARG Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 212 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN B 343 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN H 291 GLN L 243 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18614 Z= 0.203 Angle : 0.745 11.446 25527 Z= 0.358 Chirality : 0.044 0.263 3068 Planarity : 0.005 0.069 3273 Dihedral : 6.353 57.069 2804 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.59 % Allowed : 25.09 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2437 helix: -1.35 (0.44), residues: 127 sheet: -0.18 (0.18), residues: 796 loop : -2.29 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 281 HIS 0.010 0.001 HIS H 327 PHE 0.015 0.001 PHE C 75 TYR 0.014 0.001 TYR C 148 ARG 0.014 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 227 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 HIS cc_start: 0.6019 (OUTLIER) cc_final: 0.5521 (t70) REVERT: C 459 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7491 (t) REVERT: C 532 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.6114 (m-70) REVERT: E 448 ILE cc_start: 0.5600 (OUTLIER) cc_final: 0.5122 (mp) REVERT: H 315 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.8046 (t60) REVERT: K 358 GLU cc_start: 0.7869 (pt0) cc_final: 0.7597 (pt0) REVERT: K 423 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8497 (p0) REVERT: L 346 ARG cc_start: 0.6655 (ttm170) cc_final: 0.6432 (ttm-80) outliers start: 105 outliers final: 55 residues processed: 295 average time/residue: 1.2379 time to fit residues: 409.8782 Evaluate side-chains 256 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 532 HIS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 378 ASP Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 0.0980 chunk 58 optimal weight: 0.0870 chunk 237 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 402 GLN B 343 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN K 362 ASN ** L 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18614 Z= 0.213 Angle : 0.733 11.015 25527 Z= 0.352 Chirality : 0.043 0.250 3068 Planarity : 0.005 0.061 3273 Dihedral : 6.093 59.505 2804 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.90 % Allowed : 26.64 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2437 helix: -1.11 (0.46), residues: 127 sheet: 0.04 (0.18), residues: 792 loop : -2.19 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 281 HIS 0.024 0.001 HIS L 243 PHE 0.014 0.001 PHE C 75 TYR 0.013 0.001 TYR C 148 ARG 0.006 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 207 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5554 (t70) REVERT: C 459 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7490 (t) REVERT: C 532 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.6147 (m-70) REVERT: E 255 ASP cc_start: 0.6063 (OUTLIER) cc_final: 0.4865 (p0) REVERT: E 448 ILE cc_start: 0.5569 (OUTLIER) cc_final: 0.5127 (mp) REVERT: H 315 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.8102 (t60) REVERT: K 358 GLU cc_start: 0.7888 (pt0) cc_final: 0.7557 (pt0) REVERT: K 445 GLN cc_start: 0.8454 (tt0) cc_final: 0.7937 (tt0) REVERT: L 346 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6367 (ttm-80) REVERT: L 433 MET cc_start: 0.6111 (mpm) cc_final: 0.5632 (mmp) outliers start: 92 outliers final: 53 residues processed: 268 average time/residue: 1.2485 time to fit residues: 376.4741 Evaluate side-chains 252 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 192 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 532 HIS Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 247 SER Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 378 ASP Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 346 ARG Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 173 optimal weight: 0.0170 chunk 134 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 243 HIS L 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18614 Z= 0.252 Angle : 0.745 10.776 25527 Z= 0.359 Chirality : 0.044 0.247 3068 Planarity : 0.005 0.053 3273 Dihedral : 6.002 58.634 2804 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.33 % Allowed : 26.80 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2437 helix: -1.11 (0.46), residues: 127 sheet: -0.06 (0.18), residues: 817 loop : -2.15 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 281 HIS 0.009 0.001 HIS H 327 PHE 0.017 0.001 PHE C 75 TYR 0.012 0.001 TYR C 148 ARG 0.006 0.000 ARG K 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 201 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 459 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7534 (t) REVERT: C 532 HIS cc_start: 0.6362 (OUTLIER) cc_final: 0.6006 (m-70) REVERT: D 70 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8904 (ptpp) REVERT: E 255 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.4820 (p0) REVERT: E 448 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5303 (mp) REVERT: H 315 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.8200 (t60) REVERT: H 368 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8471 (t) REVERT: K 358 GLU cc_start: 0.7947 (pt0) cc_final: 0.7643 (pt0) REVERT: K 414 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8503 (p) REVERT: L 433 MET cc_start: 0.6079 (mpm) cc_final: 0.5562 (mmp) outliers start: 100 outliers final: 62 residues processed: 274 average time/residue: 1.1708 time to fit residues: 362.4843 Evaluate side-chains 254 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 184 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 532 HIS Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 340 LYS Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 247 SER Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 378 ASP Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 255 ASP Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN B 343 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN L 243 HIS ** L 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18614 Z= 0.285 Angle : 0.780 14.712 25527 Z= 0.375 Chirality : 0.044 0.249 3068 Planarity : 0.005 0.051 3273 Dihedral : 6.038 55.512 2804 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.22 % Allowed : 27.65 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.17), residues: 2437 helix: -1.04 (0.47), residues: 127 sheet: -0.05 (0.18), residues: 811 loop : -2.18 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 281 HIS 0.010 0.001 HIS K 317 PHE 0.017 0.001 PHE C 75 TYR 0.013 0.001 TYR C 148 ARG 0.014 0.001 ARG F 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 198 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 HIS cc_start: 0.6029 (OUTLIER) cc_final: 0.5354 (t70) REVERT: C 459 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7761 (t) REVERT: C 532 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.6005 (m-70) REVERT: D 70 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8917 (ptpp) REVERT: E 255 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.4688 (p0) REVERT: E 445 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: E 448 ILE cc_start: 0.5758 (OUTLIER) cc_final: 0.5436 (mp) REVERT: H 315 TRP cc_start: 0.8644 (OUTLIER) cc_final: 0.8175 (t60) REVERT: H 368 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8525 (t) REVERT: K 338 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5946 (pp) REVERT: L 433 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5716 (mmp) outliers start: 98 outliers final: 64 residues processed: 269 average time/residue: 1.2059 time to fit residues: 366.6601 Evaluate side-chains 261 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 186 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 532 HIS Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 GLN Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 378 ASP Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 255 ASP Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN B 343 ASN ** B 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN L 243 HIS ** L 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18614 Z= 0.365 Angle : 0.829 15.942 25527 Z= 0.401 Chirality : 0.045 0.253 3068 Planarity : 0.005 0.067 3273 Dihedral : 6.204 54.855 2804 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.95 % Allowed : 28.18 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2437 helix: -1.10 (0.44), residues: 133 sheet: -0.18 (0.18), residues: 816 loop : -2.20 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 383 HIS 0.019 0.002 HIS K 317 PHE 0.022 0.002 PHE K 345 TYR 0.013 0.001 TYR C 541 ARG 0.014 0.001 ARG F 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 190 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 459 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.7779 (t) REVERT: C 532 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.6043 (m-70) REVERT: D 70 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8934 (ptpp) REVERT: E 255 ASP cc_start: 0.6001 (OUTLIER) cc_final: 0.5700 (p0) REVERT: E 258 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6509 (tp) REVERT: E 448 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5657 (mp) REVERT: H 315 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.8171 (t60) REVERT: H 368 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8586 (t) REVERT: L 411 TYR cc_start: 0.6202 (m-10) cc_final: 0.5635 (m-10) REVERT: L 433 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6008 (mmp) outliers start: 93 outliers final: 61 residues processed: 256 average time/residue: 1.1609 time to fit residues: 336.9167 Evaluate side-chains 248 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 178 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 532 HIS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 288 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 255 ASP Chi-restraints excluded: chain L residue 315 TRP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 3.9990 chunk 232 optimal weight: 0.0970 chunk 142 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN C 68 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN L 243 HIS ** L 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18614 Z= 0.214 Angle : 0.771 16.007 25527 Z= 0.369 Chirality : 0.044 0.249 3068 Planarity : 0.005 0.060 3273 Dihedral : 5.803 58.638 2804 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.20 % Allowed : 30.21 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 2437 helix: -1.04 (0.44), residues: 139 sheet: 0.04 (0.18), residues: 806 loop : -2.10 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 281 HIS 0.012 0.001 HIS H 327 PHE 0.021 0.001 PHE K 345 TYR 0.011 0.001 TYR C 148 ARG 0.015 0.001 ARG F 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 196 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: C 459 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7621 (t) REVERT: C 461 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8018 (mmtt) REVERT: C 532 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.5965 (m-70) REVERT: D 70 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8826 (ptpp) REVERT: E 255 ASP cc_start: 0.5829 (OUTLIER) cc_final: 0.4631 (p0) REVERT: E 258 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6517 (tp) REVERT: E 448 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5525 (mp) REVERT: H 368 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8511 (t) REVERT: K 385 GLN cc_start: 0.7365 (tm-30) cc_final: 0.7127 (tm-30) REVERT: L 411 TYR cc_start: 0.6346 (m-10) cc_final: 0.5656 (m-10) REVERT: L 433 MET cc_start: 0.6424 (mpm) cc_final: 0.5958 (mmp) outliers start: 60 outliers final: 39 residues processed: 242 average time/residue: 1.1896 time to fit residues: 325.9207 Evaluate side-chains 231 residues out of total 2113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 532 HIS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 255 ASP Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS H 291 GLN ** L 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094892 restraints weight = 47064.866| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.40 r_work: 0.3362 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18614 Z= 0.229 Angle : 0.760 15.609 25527 Z= 0.364 Chirality : 0.044 0.244 3068 Planarity : 0.005 0.063 3273 Dihedral : 5.732 58.734 2804 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.14 % Allowed : 30.37 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2437 helix: -0.83 (0.46), residues: 128 sheet: 0.07 (0.18), residues: 813 loop : -2.07 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 315 HIS 0.009 0.001 HIS H 327 PHE 0.021 0.001 PHE K 345 TYR 0.012 0.001 TYR C 148 ARG 0.014 0.001 ARG F 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7189.19 seconds wall clock time: 128 minutes 13.18 seconds (7693.18 seconds total)