Starting phenix.real_space_refine on Sun Mar 17 16:06:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/03_2024/6ue9_20751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/03_2024/6ue9_20751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/03_2024/6ue9_20751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/03_2024/6ue9_20751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/03_2024/6ue9_20751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue9_20751/03_2024/6ue9_20751.pdb" } resolution = 2.9 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= -0.013 sd= 0.420 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 11488 2.51 5 N 3151 2.21 5 O 3490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "G ARG 346": "NH1" <-> "NH2" Residue "G ASP 378": "OD1" <-> "OD2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "G TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K GLU 358": "OE1" <-> "OE2" Residue "L GLU 389": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18227 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: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4150 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 511} 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: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 10.40, per 1000 atoms: 0.57 Number of scatterers: 18227 At special positions: 0 Unit cell: (173.196, 148.745, 174.215, 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 3490 8.00 N 3151 7.00 C 11488 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.04 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.03 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=2.04 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=2.03 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=2.04 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=2.04 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=2.04 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 601 " - " ASN C 403 " " NAG C 604 " - " ASN C 65 " " NAG C 605 " - " ASN C 451 " " 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: 6.55 Conformation dependent library (CDL) restraints added in 3.6 seconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 55 sheets defined 9.7% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.616A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.828A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.759A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.611A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.608A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.603A pdb=" N GLU B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 359' 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 421 through 427 removed outlier: 3.741A pdb=" N LYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.652A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.777A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 246' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.691A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.775A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.631A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.535A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.637A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.661A pdb=" N LEU F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.587A pdb=" N GLY F 318 " --> pdb=" O PRO F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 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: 3.698A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.548A pdb=" N LEU G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 4.320A pdb=" N GLY G 300 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 420 through 427 removed outlier: 3.615A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.697A pdb=" N ASN E 316 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.522A pdb=" N ALA E 360 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.763A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 317 removed outlier: 3.552A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.828A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.860A 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 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 297 through 301 removed outlier: 4.539A pdb=" N GLY K 300 " --> pdb=" O ASP K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 318 Processing helix chain 'K' and resid 356 through 360 Processing helix chain 'K' and resid 421 through 427 Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.713A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 426 removed outlier: 3.931A pdb=" N TRP L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A 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: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (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: 6.304A pdb=" N ILE K 458 " --> pdb=" O ASN L 459 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER L 461 " --> pdb=" O ILE K 458 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 460 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL L 463 " --> pdb=" O VAL K 460 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 462 " --> pdb=" O VAL L 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.759A pdb=" N SER B 247 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 267 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 265 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 308 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR B 267 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 306 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 269 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL B 304 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 320 through 325 removed outlier: 3.517A pdb=" N ALA B 325 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A 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: 6.453A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.575A pdb=" N ILE C 79 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 125 removed outlier: 6.571A pdb=" N TYR C 122 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU C 220 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.970A 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 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.559A pdb=" N LEU C 201 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.123A pdb=" N GLU C 225 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE C 327 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 227 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.200A 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 Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.260A pdb=" N VAL C 341 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 440 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C 343 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 349 through 354 removed outlier: 3.517A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.587A 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 461 Processing sheet with id=AC4, first strand: chain 'C' and resid 474 through 479 removed outlier: 3.775A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 525 " --> pdb=" O CYS C 478 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.893A 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: 5.460A pdb=" N VAL D 7 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 20 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN E 459 " --> pdb=" O VAL H 460 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL H 462 " --> pdb=" O ASN E 459 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER E 461 " --> pdb=" O VAL H 462 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 77 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 249 removed outlier: 3.651A pdb=" N ARG F 245 " --> pdb=" O THR F 269 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 269 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 324 through 325 Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A 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: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A 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 245 through 249 removed outlier: 3.744A pdb=" N ARG G 245 " --> pdb=" O THR G 269 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS G 249 " --> pdb=" O THR G 265 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR G 265 " --> pdb=" O HIS G 249 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 264 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 278 through 281 Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD9, first strand: chain 'E' and resid 245 through 248 removed outlier: 4.240A pdb=" N ARG E 245 " --> pdb=" O THR E 269 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 269 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 268 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLY E 270 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR E 302 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 290 through 291 removed outlier: 4.622A pdb=" N VAL E 290 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL E 307 " --> pdb=" O VAL E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 396 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AE5, first strand: chain 'E' and resid 384 through 385 Processing sheet with id=AE6, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.505A pdb=" N ARG H 245 " --> pdb=" O THR H 269 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 280 through 281 Processing sheet with id=AE8, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AE9, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AF3, first strand: chain 'K' and resid 246 through 248 removed outlier: 4.076A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 290 " --> pdb=" O VAL K 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.642A pdb=" N THR K 278 " --> pdb=" O ALA K 326 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR K 410 " --> pdb=" O GLU K 403 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.526A pdb=" N SER K 431 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.951A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L 370 " --> pdb=" O HIS L 350 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU L 352 " --> pdb=" O THR L 368 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 388 through 389 removed outlier: 3.637A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 401 through 403 removed outlier: 3.692A pdb=" N ARG L 401 " --> pdb=" O ALA L 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 412 " --> pdb=" O ARG L 401 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR L 410 " --> pdb=" O GLU L 403 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 7.15 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: 5888 1.34 - 1.46: 4375 1.46 - 1.59: 8280 1.59 - 1.71: 0 1.71 - 1.84: 115 Bond restraints: 18658 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" C THR D 54 " pdb=" N SER D 55 " ideal model delta sigma weight residual 1.327 1.300 0.027 1.05e-02 9.07e+03 6.40e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 18653 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.87: 622 105.87 - 112.95: 10424 112.95 - 120.03: 5896 120.03 - 127.11: 8327 127.11 - 134.20: 317 Bond angle restraints: 25586 Sorted by residual: angle pdb=" N SER D 55 " pdb=" CA SER D 55 " pdb=" C SER D 55 " ideal model delta sigma weight residual 108.13 99.01 9.12 9.00e-01 1.23e+00 1.03e+02 angle pdb=" C ASN C 329 " pdb=" N GLU C 330 " pdb=" CA GLU C 330 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta sigma weight residual 120.39 127.45 -7.06 1.39e+00 5.18e-01 2.58e+01 angle pdb=" N VAL C 158 " pdb=" CA VAL C 158 " pdb=" C VAL C 158 " ideal model delta sigma weight residual 113.20 108.46 4.74 9.60e-01 1.09e+00 2.43e+01 angle pdb=" CA SER A 260 " pdb=" C SER A 260 " pdb=" N GLU A 261 " ideal model delta sigma weight residual 116.84 125.20 -8.36 1.71e+00 3.42e-01 2.39e+01 ... (remaining 25581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.88: 10366 19.88 - 39.75: 811 39.75 - 59.63: 121 59.63 - 79.51: 18 79.51 - 99.39: 18 Dihedral angle restraints: 11334 sinusoidal: 4230 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS K 299 " pdb=" SG CYS K 299 " pdb=" SG CYS L 242 " pdb=" CB CYS L 242 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 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 3.83 89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual -86.00 -158.33 72.33 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 11331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2647 0.085 - 0.170: 391 0.170 - 0.254: 32 0.254 - 0.339: 5 0.339 - 0.424: 5 Chirality restraints: 3080 Sorted by residual: chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 451 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 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 -2.08 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE E 448 " pdb=" CA ILE E 448 " pdb=" CG1 ILE E 448 " pdb=" CG2 ILE E 448 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 3077 not shown) Planarity restraints: 3287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 403 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO F 404 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 404 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 404 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 327 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 328 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 375 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO L 376 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 376 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 376 " 0.039 5.00e-02 4.00e+02 ... (remaining 3284 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3153 2.77 - 3.30: 14380 3.30 - 3.84: 26867 3.84 - 4.37: 28681 4.37 - 4.90: 54365 Nonbonded interactions: 127446 Sorted by model distance: nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.241 2.440 nonbonded pdb=" O THR H 280 " pdb=" OG1 THR H 324 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR L 320 " pdb=" OD1 ASN L 337 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR C 122 " pdb=" OD1 ASN C 133 " model vdw 2.292 2.440 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.318 2.520 ... (remaining 127441 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: 2.710 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: 13.050 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 49.600 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3798 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 18658 Z= 0.448 Angle : 1.049 16.113 25586 Z= 0.558 Chirality : 0.062 0.424 3080 Planarity : 0.008 0.075 3278 Dihedral : 14.612 99.386 6625 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 0.32 % Allowed : 9.85 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.09 % 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: -3.87 (0.14), residues: 2439 helix: -4.23 (0.21), residues: 143 sheet: -1.61 (0.16), residues: 863 loop : -3.14 (0.13), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 315 HIS 0.007 0.001 HIS K 243 PHE 0.031 0.003 PHE C 136 TYR 0.019 0.003 TYR G 395 ARG 0.005 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 539 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 327 HIS cc_start: 0.4382 (p90) cc_final: 0.4129 (p90) REVERT: K 365 VAL cc_start: 0.4065 (m) cc_final: 0.3548 (m) outliers start: 6 outliers final: 3 residues processed: 544 average time/residue: 0.9770 time to fit residues: 612.4835 Evaluate side-chains 261 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 393 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 406 GLN C 209 ASN D 11 ASN D 30 ASN D 37 ASN D 90 ASN F 362 ASN F 459 ASN G 263 ASN G 291 GLN ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN E 459 ASN H 243 HIS H 249 HIS H 316 ASN ** H 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN K 243 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN K 457 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4910 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18658 Z= 0.314 Angle : 0.957 12.541 25586 Z= 0.454 Chirality : 0.050 0.364 3080 Planarity : 0.007 0.072 3278 Dihedral : 8.694 68.814 2855 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 7.29 % Allowed : 20.50 % Favored : 72.20 % 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: -3.08 (0.15), residues: 2439 helix: -3.37 (0.28), residues: 144 sheet: -0.90 (0.17), residues: 834 loop : -2.74 (0.14), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 431 HIS 0.007 0.001 HIS C 310 PHE 0.029 0.002 PHE C 75 TYR 0.016 0.002 TYR D 110 ARG 0.008 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 342 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 VAL cc_start: 0.3172 (t) cc_final: 0.2941 (t) REVERT: F 433 MET cc_start: 0.2626 (tpt) cc_final: 0.1936 (tpt) REVERT: G 322 THR cc_start: 0.6483 (m) cc_final: 0.6270 (m) REVERT: E 291 GLN cc_start: 0.6473 (pp30) cc_final: 0.6115 (tm130) REVERT: E 402 GLN cc_start: 0.7558 (tp40) cc_final: 0.7320 (tp40) REVERT: L 365 VAL cc_start: 0.6949 (OUTLIER) cc_final: 0.6728 (p) outliers start: 137 outliers final: 56 residues processed: 439 average time/residue: 0.7913 time to fit residues: 410.8918 Evaluate side-chains 330 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 273 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 424 TRP Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 416 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 222 optimal weight: 0.0020 chunk 240 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN C 530 GLN ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS H 243 HIS H 457 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 18658 Z= 0.296 Angle : 0.878 12.970 25586 Z= 0.421 Chirality : 0.049 0.383 3080 Planarity : 0.006 0.078 3278 Dihedral : 6.737 55.114 2848 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 8.04 % Allowed : 22.63 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.46 (0.16), residues: 2439 helix: -2.25 (0.36), residues: 149 sheet: -0.38 (0.18), residues: 785 loop : -2.41 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 523 HIS 0.023 0.002 HIS K 317 PHE 0.022 0.002 PHE L 374 TYR 0.025 0.002 TYR C 90 ARG 0.012 0.001 ARG C 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 368 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.4891 (t-90) REVERT: G 377 LYS cc_start: 0.5606 (OUTLIER) cc_final: 0.4595 (tmmm) REVERT: K 253 LEU cc_start: 0.7810 (mm) cc_final: 0.6395 (tp) REVERT: L 327 HIS cc_start: 0.1798 (m-70) cc_final: 0.1081 (t70) REVERT: L 411 TYR cc_start: 0.3326 (m-80) cc_final: 0.2118 (m-80) REVERT: L 430 PHE cc_start: 0.4204 (m-80) cc_final: 0.3877 (m-80) outliers start: 151 outliers final: 60 residues processed: 472 average time/residue: 0.8419 time to fit residues: 466.9208 Evaluate side-chains 347 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 285 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 368 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 456 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 212 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 445 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN D 88 GLN D 90 ASN E 459 ASN H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.9817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 18658 Z= 0.422 Angle : 1.009 14.783 25586 Z= 0.483 Chirality : 0.054 0.388 3080 Planarity : 0.007 0.065 3278 Dihedral : 6.951 59.935 2848 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.37 % Rotamer: Outliers : 9.00 % Allowed : 24.12 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.39 (0.16), residues: 2439 helix: -1.75 (0.40), residues: 151 sheet: -0.45 (0.18), residues: 783 loop : -2.32 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 383 HIS 0.016 0.002 HIS B 243 PHE 0.031 0.003 PHE A 374 TYR 0.029 0.003 TYR D 102 ARG 0.030 0.001 ARG H 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 411 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 346 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5598 (pmm-80) REVERT: G 375 SER cc_start: 0.6676 (OUTLIER) cc_final: 0.6344 (t) REVERT: G 414 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7118 (t) REVERT: E 378 ASP cc_start: 0.7737 (t0) cc_final: 0.7529 (t0) REVERT: E 402 GLN cc_start: 0.8158 (tp40) cc_final: 0.7945 (tp40) REVERT: H 464 MET cc_start: 0.6924 (tpt) cc_final: 0.6660 (tpp) REVERT: K 291 GLN cc_start: 0.6516 (pp30) cc_final: 0.6163 (pp30) REVERT: K 368 THR cc_start: 0.8252 (m) cc_final: 0.7909 (p) outliers start: 169 outliers final: 61 residues processed: 525 average time/residue: 0.9311 time to fit residues: 564.9682 Evaluate side-chains 389 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 325 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 340 LYS Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 176 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN B 313 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 HIS F 243 HIS F 445 GLN F 457 HIS G 291 GLN G 445 GLN E 263 ASN H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 1.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18658 Z= 0.279 Angle : 0.888 21.479 25586 Z= 0.412 Chirality : 0.048 0.365 3080 Planarity : 0.005 0.055 3278 Dihedral : 6.181 55.070 2848 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 6.87 % Allowed : 29.82 % Favored : 63.31 % 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: -2.19 (0.16), residues: 2439 helix: -1.72 (0.39), residues: 162 sheet: -0.28 (0.18), residues: 814 loop : -2.23 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 424 HIS 0.007 0.001 HIS F 457 PHE 0.020 0.002 PHE L 374 TYR 0.019 0.002 TYR D 102 ARG 0.019 0.001 ARG E 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 336 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 505 ASN cc_start: 0.5674 (OUTLIER) cc_final: 0.5445 (m110) REVERT: D 129 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8093 (mt) REVERT: F 335 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6376 (p) REVERT: G 375 SER cc_start: 0.6673 (OUTLIER) cc_final: 0.6404 (t) REVERT: E 378 ASP cc_start: 0.7660 (t0) cc_final: 0.7447 (t0) REVERT: K 291 GLN cc_start: 0.6850 (pp30) cc_final: 0.6390 (pp30) REVERT: K 372 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.5804 (tmt90) outliers start: 129 outliers final: 74 residues processed: 420 average time/residue: 1.0481 time to fit residues: 506.5204 Evaluate side-chains 368 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 289 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 340 LYS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 372 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 424 TRP Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 372 ARG Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 456 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 58 optimal weight: 0.8980 chunk 237 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN C 481 ASN F 316 ASN F 343 ASN F 445 GLN F 457 HIS G 249 HIS H 243 HIS K 350 HIS ** K 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS L 385 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 1.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18658 Z= 0.214 Angle : 0.832 20.887 25586 Z= 0.383 Chirality : 0.046 0.364 3080 Planarity : 0.005 0.057 3278 Dihedral : 5.838 55.879 2848 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.80 % Allowed : 32.06 % Favored : 62.14 % 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: -1.95 (0.16), residues: 2439 helix: -1.51 (0.38), residues: 166 sheet: -0.22 (0.17), residues: 828 loop : -2.01 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 424 HIS 0.007 0.001 HIS G 249 PHE 0.019 0.001 PHE E 430 TYR 0.017 0.001 TYR C 60 ARG 0.011 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 311 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 441 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7774 (tp) REVERT: C 175 LEU cc_start: 0.0039 (OUTLIER) cc_final: -0.0194 (mm) REVERT: F 316 ASN cc_start: 0.7442 (t0) cc_final: 0.7171 (p0) REVERT: G 375 SER cc_start: 0.6628 (OUTLIER) cc_final: 0.6351 (t) REVERT: E 378 ASP cc_start: 0.7425 (t0) cc_final: 0.7180 (t0) REVERT: H 423 ASP cc_start: 0.7722 (p0) cc_final: 0.6869 (p0) REVERT: H 437 GLU cc_start: 0.7438 (pp20) cc_final: 0.6984 (pp20) REVERT: K 291 GLN cc_start: 0.6900 (pp30) cc_final: 0.6503 (pp30) REVERT: K 372 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.5900 (ttt90) outliers start: 109 outliers final: 56 residues processed: 386 average time/residue: 0.9378 time to fit residues: 418.0857 Evaluate side-chains 346 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 286 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 372 ARG Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain L residue 351 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 0.0170 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN B 459 ASN C 501 ASN D 81 ASN F 343 ASN F 445 GLN F 457 HIS G 249 HIS E 459 ASN H 243 HIS K 350 HIS K 457 HIS L 249 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 1.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18658 Z= 0.227 Angle : 0.831 21.553 25586 Z= 0.384 Chirality : 0.046 0.357 3080 Planarity : 0.005 0.060 3278 Dihedral : 5.665 55.651 2848 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.02 % Allowed : 32.06 % Favored : 61.93 % 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 (0.16), residues: 2439 helix: -1.43 (0.39), residues: 167 sheet: -0.08 (0.18), residues: 825 loop : -1.92 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 424 HIS 0.006 0.001 HIS G 249 PHE 0.024 0.001 PHE K 279 TYR 0.012 0.001 TYR D 63 ARG 0.015 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 304 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 LEU cc_start: 0.0508 (OUTLIER) cc_final: 0.0285 (mm) REVERT: D 8 LEU cc_start: 0.8320 (tp) cc_final: 0.8118 (mt) REVERT: F 316 ASN cc_start: 0.7499 (t0) cc_final: 0.7248 (p0) REVERT: G 375 SER cc_start: 0.6893 (OUTLIER) cc_final: 0.6520 (t) REVERT: E 378 ASP cc_start: 0.7272 (t0) cc_final: 0.6969 (t0) REVERT: E 449 ASP cc_start: 0.7751 (m-30) cc_final: 0.6980 (p0) REVERT: K 291 GLN cc_start: 0.7004 (pp30) cc_final: 0.6587 (pp30) REVERT: K 348 GLU cc_start: 0.6512 (pm20) cc_final: 0.6158 (pm20) REVERT: L 367 LEU cc_start: 0.7988 (mm) cc_final: 0.7454 (pt) outliers start: 113 outliers final: 65 residues processed: 382 average time/residue: 0.9485 time to fit residues: 417.6695 Evaluate side-chains 349 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 282 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 0.0970 chunk 160 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN C 84 GLN C 150 GLN F 343 ASN H 243 HIS K 457 HIS L 385 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 1.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 18658 Z= 0.306 Angle : 0.910 24.201 25586 Z= 0.428 Chirality : 0.048 0.376 3080 Planarity : 0.005 0.058 3278 Dihedral : 6.022 56.926 2848 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.48 % Allowed : 33.55 % Favored : 60.97 % 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 (0.16), residues: 2439 helix: -1.45 (0.39), residues: 167 sheet: -0.11 (0.18), residues: 831 loop : -1.90 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 424 HIS 0.012 0.001 HIS K 317 PHE 0.023 0.002 PHE H 321 TYR 0.017 0.002 TYR D 63 ARG 0.012 0.001 ARG K 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 303 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 ASN cc_start: 0.3633 (OUTLIER) cc_final: 0.3332 (p0) REVERT: F 279 PHE cc_start: 0.6946 (m-80) cc_final: 0.6741 (m-80) REVERT: E 378 ASP cc_start: 0.7416 (t0) cc_final: 0.7150 (t0) REVERT: E 402 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7876 (tm-30) REVERT: E 433 MET cc_start: 0.6606 (tpp) cc_final: 0.5447 (tpt) REVERT: E 449 ASP cc_start: 0.7738 (m-30) cc_final: 0.7502 (p0) REVERT: H 249 HIS cc_start: 0.7388 (m-70) cc_final: 0.7159 (m-70) REVERT: K 291 GLN cc_start: 0.7159 (pp30) cc_final: 0.6812 (pp30) REVERT: L 365 VAL cc_start: 0.7910 (t) cc_final: 0.7576 (p) outliers start: 103 outliers final: 55 residues processed: 380 average time/residue: 1.0186 time to fit residues: 444.4473 Evaluate side-chains 316 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain L residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 2.9990 chunk 226 optimal weight: 0.4980 chunk 206 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 ASN D 90 ASN H 243 HIS K 249 HIS K 457 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 1.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 18658 Z= 0.358 Angle : 0.964 26.289 25586 Z= 0.456 Chirality : 0.050 0.372 3080 Planarity : 0.006 0.061 3278 Dihedral : 6.259 55.323 2848 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.85 % Allowed : 35.04 % Favored : 60.12 % 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: -1.96 (0.16), residues: 2439 helix: -1.79 (0.38), residues: 165 sheet: -0.28 (0.18), residues: 840 loop : -1.95 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 315 HIS 0.016 0.001 HIS K 317 PHE 0.032 0.002 PHE K 345 TYR 0.018 0.002 TYR K 395 ARG 0.008 0.001 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 290 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6980 (m-40) REVERT: C 140 ASN cc_start: 0.4280 (OUTLIER) cc_final: 0.3994 (p0) REVERT: G 306 SER cc_start: 0.6270 (OUTLIER) cc_final: 0.6067 (p) REVERT: G 422 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5464 (tm-30) REVERT: E 378 ASP cc_start: 0.7710 (t0) cc_final: 0.7503 (t0) REVERT: E 402 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 433 MET cc_start: 0.6983 (tpp) cc_final: 0.5865 (tpt) REVERT: H 249 HIS cc_start: 0.8077 (m-70) cc_final: 0.7861 (m-70) REVERT: K 291 GLN cc_start: 0.7421 (pp30) cc_final: 0.7158 (pp30) REVERT: K 385 GLN cc_start: 0.7056 (pm20) cc_final: 0.6855 (pp30) REVERT: K 429 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6853 (t) outliers start: 91 outliers final: 52 residues processed: 358 average time/residue: 1.1034 time to fit residues: 448.0867 Evaluate side-chains 298 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 242 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 280 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 243 HIS K 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 1.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 18658 Z= 0.368 Angle : 0.965 26.222 25586 Z= 0.455 Chirality : 0.049 0.366 3080 Planarity : 0.006 0.064 3278 Dihedral : 6.271 55.435 2848 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.99 % Allowed : 37.17 % Favored : 58.84 % 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: -1.96 (0.16), residues: 2439 helix: -1.34 (0.40), residues: 159 sheet: -0.35 (0.17), residues: 863 loop : -1.98 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 315 HIS 0.008 0.001 HIS F 457 PHE 0.027 0.002 PHE K 345 TYR 0.022 0.002 TYR E 411 ARG 0.019 0.001 ARG F 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 250 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 403 GLU cc_start: 0.7916 (mp0) cc_final: 0.7557 (mp0) REVERT: E 402 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8121 (tm-30) REVERT: E 433 MET cc_start: 0.6889 (tpp) cc_final: 0.5786 (tpt) REVERT: H 249 HIS cc_start: 0.8273 (m-70) cc_final: 0.8019 (m-70) REVERT: K 291 GLN cc_start: 0.7524 (pp30) cc_final: 0.7237 (pp30) REVERT: L 433 MET cc_start: 0.6881 (ppp) cc_final: 0.6396 (ptm) outliers start: 75 outliers final: 51 residues processed: 307 average time/residue: 1.2003 time to fit residues: 415.3539 Evaluate side-chains 280 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 0.9980 chunk 207 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 243 HIS K 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.118213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083508 restraints weight = 47412.981| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.31 r_work: 0.3252 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 1.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18658 Z= 0.236 Angle : 0.921 25.450 25586 Z= 0.427 Chirality : 0.047 0.356 3080 Planarity : 0.006 0.080 3278 Dihedral : 5.899 59.276 2848 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.18 % Allowed : 39.08 % Favored : 58.73 % 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: -1.74 (0.16), residues: 2439 helix: -1.21 (0.40), residues: 160 sheet: -0.15 (0.18), residues: 844 loop : -1.85 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 315 HIS 0.010 0.001 HIS G 243 PHE 0.015 0.001 PHE L 374 TYR 0.019 0.001 TYR E 411 ARG 0.021 0.001 ARG B 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7875.05 seconds wall clock time: 139 minutes 21.53 seconds (8361.53 seconds total)