Starting phenix.real_space_refine on Mon Feb 19 08:53:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2024/8h12_34422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2024/8h12_34422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44681 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2024/8h12_34422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2024/8h12_34422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2024/8h12_34422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2024/8h12_34422.pdb" } resolution = 3.44681 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 129 5.16 5 C 15433 2.51 5 N 3955 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1121": "OD1" <-> "OD2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1023": "OD1" <-> "OD2" Residue "B PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1074": "OE1" <-> "OE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 376": "OD1" <-> "OD2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 480": "OD1" <-> "OD2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C ASP 649": "OD1" <-> "OD2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 849": "OD1" <-> "OD2" Residue "C TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 900": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 972": "OE1" <-> "OE2" Residue "C PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1074": "OE1" <-> "OE2" Residue "C PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1100": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24221 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7861 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 6 Chain: "B" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7861 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 6 Chain: "C" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7869 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 49, 'TRANS': 958} Chain breaks: 6 Chain: "D" 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: "E" 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: "F" 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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 12.59, per 1000 atoms: 0.52 Number of scatterers: 24221 At special positions: 0 Unit cell: (124.2, 126.9, 172.8, 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 129 16.00 O 4704 8.00 N 3955 7.00 C 15433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS C 969 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 969 " - pdb=" SG CYS B 400 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 969 " - pdb=" SG CYS C 400 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1201 " - " ASN A 65 " " NAG A1202 " - " ASN A1080 " " NAG A1203 " - " ASN A 109 " " NAG A1204 " - " ASN A 119 " " NAG A1205 " - " ASN A 158 " " NAG A1206 " - " ASN A 269 " " NAG A1207 " - " ASN A 318 " " NAG A1208 " - " ASN A 357 " " NAG A1209 " - " ASN A 602 " " NAG A1210 " - " ASN A 691 " " NAG A1211 " - " ASN A 699 " " NAG A1212 " - " ASN A 783 " " NAG A1213 " - " ASN A1056 " " NAG B1201 " - " ASN B 65 " " NAG B1202 " - " ASN B1080 " " NAG B1203 " - " ASN B 109 " " NAG B1204 " - " ASN B 119 " " NAG B1205 " - " ASN B 158 " " NAG B1206 " - " ASN B 269 " " NAG B1207 " - " ASN B 318 " " NAG B1208 " - " ASN B 357 " " NAG B1209 " - " ASN B 602 " " NAG B1210 " - " ASN B 691 " " NAG B1211 " - " ASN B 699 " " NAG B1212 " - " ASN B 783 " " NAG B1213 " - " ASN B1056 " " NAG C1201 " - " ASN C 65 " " NAG C1202 " - " ASN C1080 " " NAG C1203 " - " ASN C 109 " " NAG C1204 " - " ASN C 119 " " NAG C1205 " - " ASN C 158 " " NAG C1206 " - " ASN C 269 " " NAG C1207 " - " ASN C 318 " " NAG C1208 " - " ASN C 357 " " NAG C1209 " - " ASN C 602 " " NAG C1210 " - " ASN C 691 " " NAG C1211 " - " ASN C 699 " " NAG C1212 " - " ASN C 783 " " NAG C1213 " - " ASN C1056 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 11.23 Conformation dependent library (CDL) restraints added in 4.5 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 45 sheets defined 24.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.600A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.688A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.809A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.513A pdb=" N GLN A 492 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.516A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 removed outlier: 3.771A pdb=" N LEU A 615 " --> pdb=" O ALA A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.869A pdb=" N SER A 623 " --> pdb=" O ARG A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.659A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.802A pdb=" N ALA A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.577A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 855 through 864 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.770A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.542A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.885A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 940 " --> pdb=" O GLN A 936 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.603A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1015 removed outlier: 3.700A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 986 " --> pdb=" O ARG A 982 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.699A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.571A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.545A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.589A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.793A pdb=" N LEU B 615 " --> pdb=" O ALA B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.625A pdb=" N SER B 623 " --> pdb=" O ARG B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.529A pdb=" N LEU B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 765 removed outlier: 3.962A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 764 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 832 through 837 Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.749A pdb=" N ALA B 857 " --> pdb=" O ALA B 853 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 858 " --> pdb=" O ALA B 854 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 861 " --> pdb=" O ALA B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 removed outlier: 3.675A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.655A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.588A pdb=" N GLN B 908 " --> pdb=" O GLN B 904 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 916 " --> pdb=" O ALA B 912 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 917 " --> pdb=" O ILE B 913 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.384A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 963 removed outlier: 3.535A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1015 removed outlier: 4.385A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.619A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.727A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 3.504A pdb=" N ASP C 393 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.553A pdb=" N HIS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.796A pdb=" N LEU C 615 " --> pdb=" O ALA C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 742 through 765 removed outlier: 3.769A pdb=" N ALA C 748 " --> pdb=" O GLN C 744 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 832 through 837 Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.557A pdb=" N ALA C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 857 " --> pdb=" O ALA C 853 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 860 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 861 " --> pdb=" O ALA C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 removed outlier: 3.521A pdb=" N ALA C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.381A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 921 removed outlier: 3.710A pdb=" N ILE C 916 " --> pdb=" O ALA C 912 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 917 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.018A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.993A pdb=" N SER C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1015 removed outlier: 4.071A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.713A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.876A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.084A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.546A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.855A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 540 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.845A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.670A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 710 removed outlier: 6.638A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA A1037 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A1043 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.642A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.696A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.502A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.885A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.178A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 315 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.698A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 540 removed outlier: 3.604A pdb=" N SER B 574 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.546A pdb=" N ILE B 656 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.578A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 694 through 710 removed outlier: 6.635A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B1034 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.675A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD3, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.507A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS B1064 " --> pdb=" O ILE B1115 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD5, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.650A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.829A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.132A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 127 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AD9, first strand: chain 'C' and resid 312 through 315 Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.789A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE3, first strand: chain 'C' and resid 537 through 540 removed outlier: 3.874A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 640 through 641 Processing sheet with id=AE5, first strand: chain 'C' and resid 694 through 710 removed outlier: 6.678A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.615A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE8, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.830A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1076 through 1079 863 hydrogen bonds defined for protein. 2340 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: 9.93 Time building geometry restraints manager: 11.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7675 1.35 - 1.47: 6569 1.47 - 1.60: 10349 1.60 - 1.73: 0 1.73 - 1.86: 171 Bond restraints: 24764 Sorted by residual: bond pdb=" C1 NAG C1209 " pdb=" O5 NAG C1209 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 NAG B1209 " pdb=" O5 NAG B1209 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C1 NAG A1209 " pdb=" O5 NAG A1209 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" CB CYS B 969 " pdb=" SG CYS B 969 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.73e+00 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.51e+00 ... (remaining 24759 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 487 105.52 - 112.64: 12878 112.64 - 119.77: 7919 119.77 - 126.90: 12177 126.90 - 134.03: 225 Bond angle restraints: 33686 Sorted by residual: angle pdb=" CA CYS A 159 " pdb=" CB CYS A 159 " pdb=" SG CYS A 159 " ideal model delta sigma weight residual 114.40 126.97 -12.57 2.30e+00 1.89e-01 2.99e+01 angle pdb=" CA CYS A 511 " pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " ideal model delta sigma weight residual 114.40 125.53 -11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" C ASN B 158 " pdb=" N CYS B 159 " pdb=" CA CYS B 159 " ideal model delta sigma weight residual 122.21 114.89 7.32 1.62e+00 3.81e-01 2.04e+01 angle pdb=" CA CYS B 511 " pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " ideal model delta sigma weight residual 114.40 124.72 -10.32 2.30e+00 1.89e-01 2.01e+01 angle pdb=" CA CYS C 511 " pdb=" CB CYS C 511 " pdb=" SG CYS C 511 " ideal model delta sigma weight residual 114.40 124.72 -10.32 2.30e+00 1.89e-01 2.01e+01 ... (remaining 33681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13867 17.86 - 35.72: 1171 35.72 - 53.58: 248 53.58 - 71.45: 40 71.45 - 89.31: 27 Dihedral angle restraints: 15353 sinusoidal: 6539 harmonic: 8814 Sorted by residual: dihedral pdb=" CB CYS C 603 " pdb=" SG CYS C 603 " pdb=" SG CYS C 635 " pdb=" CB CYS C 635 " ideal model delta sinusoidal sigma weight residual -86.00 -8.97 -77.03 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS A 635 " pdb=" CB CYS A 635 " ideal model delta sinusoidal sigma weight residual -86.00 -30.73 -55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual 93.00 45.87 47.13 1 1.00e+01 1.00e-02 3.07e+01 ... (remaining 15350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3330 0.078 - 0.155: 583 0.155 - 0.233: 26 0.233 - 0.310: 4 0.310 - 0.388: 9 Chirality restraints: 3952 Sorted by residual: chirality pdb=" C1 NAG C1202 " pdb=" ND2 ASN C1080 " pdb=" C2 NAG C1202 " pdb=" O5 NAG C1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1 NAG B1202 " pdb=" ND2 ASN B1080 " pdb=" C2 NAG B1202 " pdb=" O5 NAG B1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C1 NAG A1206 " pdb=" ND2 ASN A 269 " pdb=" C2 NAG A1206 " pdb=" O5 NAG A1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 3949 not shown) Planarity restraints: 4331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 469 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO C 470 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 308 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO B 309 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 469 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 470 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.058 5.00e-02 4.00e+02 ... (remaining 4328 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5212 2.78 - 3.31: 19689 3.31 - 3.84: 36923 3.84 - 4.37: 43605 4.37 - 4.90: 79256 Nonbonded interactions: 184685 Sorted by model distance: nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" O LEU A 58 " model vdw 2.261 2.440 nonbonded pdb=" OD2 ASP A 44 " pdb=" NH2 ARG A 48 " model vdw 2.267 2.520 nonbonded pdb=" O ASN C 960 " pdb=" OG SER C 964 " model vdw 2.272 2.440 ... (remaining 184680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 31 through 808 or resid 831 through 1123 or resid 1201 thr \ ough 1213)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.920 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 64.860 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.006 0.072 24764 Z= 0.405 Angle : 0.813 12.567 33686 Z= 0.437 Chirality : 0.057 0.388 3952 Planarity : 0.006 0.116 4289 Dihedral : 13.958 89.307 9555 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.14), residues: 2980 helix: -2.00 (0.17), residues: 660 sheet: -0.33 (0.20), residues: 645 loop : -1.49 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 423 HIS 0.007 0.002 HIS C1046 PHE 0.041 0.003 PHE C 334 TYR 0.030 0.002 TYR C 491 ARG 0.011 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.649 Fit side-chains REVERT: A 849 ASP cc_start: 0.7876 (m-30) cc_final: 0.7644 (m-30) REVERT: A 882 MET cc_start: 0.8305 (mtp) cc_final: 0.8098 (mtm) REVERT: A 968 LYS cc_start: 0.7788 (tmtt) cc_final: 0.6949 (mttt) REVERT: B 713 MET cc_start: 0.8899 (ptt) cc_final: 0.8675 (ptt) REVERT: B 768 LYS cc_start: 0.8213 (mttt) cc_final: 0.6930 (mmpt) REVERT: B 968 LYS cc_start: 0.7375 (mtmt) cc_final: 0.6962 (tmtt) REVERT: B 1052 SER cc_start: 0.9009 (p) cc_final: 0.8261 (m) REVERT: B 1105 SER cc_start: 0.8840 (t) cc_final: 0.8514 (t) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3295 time to fit residues: 145.7850 Evaluate side-chains 218 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN B1088 GLN C 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24764 Z= 0.375 Angle : 0.642 8.936 33686 Z= 0.336 Chirality : 0.050 0.365 3952 Planarity : 0.005 0.102 4289 Dihedral : 7.600 58.280 4192 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.88 % Allowed : 7.39 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 2980 helix: -1.14 (0.18), residues: 691 sheet: -0.21 (0.21), residues: 610 loop : -1.38 (0.13), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 423 HIS 0.006 0.002 HIS C1046 PHE 0.026 0.002 PHE C 334 TYR 0.024 0.002 TYR A1049 ARG 0.006 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 2.935 Fit side-chains REVERT: A 770 MET cc_start: 0.8331 (mmm) cc_final: 0.7905 (mmm) REVERT: A 884 MET cc_start: 0.8164 (mmt) cc_final: 0.7900 (tpt) REVERT: A 936 GLN cc_start: 0.8303 (mt0) cc_final: 0.8095 (mt0) REVERT: A 937 ASN cc_start: 0.7658 (m110) cc_final: 0.7257 (m-40) REVERT: A 968 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7382 (mttt) REVERT: B 93 GLU cc_start: 0.6719 (pt0) cc_final: 0.6483 (pt0) REVERT: B 709 MET cc_start: 0.8818 (mtm) cc_final: 0.8537 (mtm) REVERT: B 713 MET cc_start: 0.9006 (ptt) cc_final: 0.8789 (ptt) REVERT: B 717 SER cc_start: 0.9029 (p) cc_final: 0.8085 (m) REVERT: B 768 LYS cc_start: 0.8174 (mttt) cc_final: 0.6896 (mmpt) REVERT: B 796 LYS cc_start: 0.7895 (mttm) cc_final: 0.7691 (mptp) REVERT: B 968 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7236 (tmtt) outliers start: 23 outliers final: 20 residues processed: 244 average time/residue: 0.3308 time to fit residues: 132.0026 Evaluate side-chains 234 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 999 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24764 Z= 0.249 Angle : 0.563 7.559 33686 Z= 0.295 Chirality : 0.048 0.364 3952 Planarity : 0.005 0.094 4289 Dihedral : 6.907 59.316 4192 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.18 % Allowed : 11.08 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 2980 helix: -0.37 (0.20), residues: 666 sheet: -0.15 (0.21), residues: 611 loop : -1.34 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 423 HIS 0.004 0.001 HIS B 611 PHE 0.022 0.002 PHE B1079 TYR 0.023 0.001 TYR A1049 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 2.798 Fit side-chains revert: symmetry clash REVERT: A 360 PHE cc_start: 0.8493 (m-80) cc_final: 0.8290 (m-80) REVERT: A 770 MET cc_start: 0.8382 (mmm) cc_final: 0.7862 (mmm) REVERT: A 937 ASN cc_start: 0.7625 (m110) cc_final: 0.7230 (m-40) REVERT: A 968 LYS cc_start: 0.8312 (tmtt) cc_final: 0.7461 (mttt) REVERT: B 224 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7109 (pp) REVERT: B 709 MET cc_start: 0.8788 (mtm) cc_final: 0.8506 (mtm) REVERT: B 717 SER cc_start: 0.8800 (p) cc_final: 0.7970 (m) REVERT: B 796 LYS cc_start: 0.8099 (mttm) cc_final: 0.7861 (mptp) REVERT: B 968 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7355 (tmtt) REVERT: C 851 MET cc_start: 0.8442 (mtm) cc_final: 0.8167 (mtt) outliers start: 31 outliers final: 24 residues processed: 263 average time/residue: 0.3196 time to fit residues: 138.9357 Evaluate side-chains 249 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.0040 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24764 Z= 0.160 Angle : 0.508 7.764 33686 Z= 0.267 Chirality : 0.046 0.370 3952 Planarity : 0.004 0.090 4289 Dihedral : 6.286 59.720 4192 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.68 % Allowed : 12.87 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2980 helix: 0.25 (0.21), residues: 654 sheet: -0.10 (0.21), residues: 605 loop : -1.22 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.002 0.001 HIS B 181 PHE 0.023 0.001 PHE B 220 TYR 0.029 0.001 TYR B 163 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.888 Fit side-chains REVERT: A 181 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.6821 (p90) REVERT: A 770 MET cc_start: 0.8419 (mmm) cc_final: 0.7883 (mmm) REVERT: A 937 ASN cc_start: 0.7524 (m110) cc_final: 0.7113 (m-40) REVERT: A 968 LYS cc_start: 0.8287 (tmtt) cc_final: 0.7408 (mttt) REVERT: A 1020 LYS cc_start: 0.8597 (mttp) cc_final: 0.8277 (mttp) REVERT: A 1080 ASN cc_start: 0.6974 (t0) cc_final: 0.6758 (t0) REVERT: B 224 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7031 (pp) REVERT: B 562 VAL cc_start: 0.8926 (p) cc_final: 0.8657 (t) REVERT: B 589 ASN cc_start: 0.8261 (p0) cc_final: 0.7982 (p0) REVERT: B 709 MET cc_start: 0.8803 (mtm) cc_final: 0.8495 (mtm) REVERT: B 717 SER cc_start: 0.8648 (p) cc_final: 0.7925 (m) REVERT: B 796 LYS cc_start: 0.8015 (mttm) cc_final: 0.7753 (mptp) REVERT: B 888 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: B 968 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6842 (tmtt) REVERT: C 421 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8642 (pt) REVERT: C 851 MET cc_start: 0.8384 (mtm) cc_final: 0.8131 (mtt) REVERT: C 999 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.7040 (tt0) outliers start: 44 outliers final: 28 residues processed: 273 average time/residue: 0.3410 time to fit residues: 152.9915 Evaluate side-chains 268 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN B 201 GLN B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN C 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 24764 Z= 0.477 Angle : 0.676 8.116 33686 Z= 0.352 Chirality : 0.052 0.342 3952 Planarity : 0.005 0.087 4289 Dihedral : 6.715 59.827 4192 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.36 % Allowed : 13.86 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 2980 helix: -0.31 (0.20), residues: 671 sheet: -0.21 (0.21), residues: 604 loop : -1.40 (0.13), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 423 HIS 0.008 0.002 HIS B 611 PHE 0.028 0.003 PHE C 220 TYR 0.026 0.002 TYR A1049 ARG 0.007 0.001 ARG A1089 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 229 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8147 (p) REVERT: A 181 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.6951 (p90) REVERT: A 770 MET cc_start: 0.8436 (mmm) cc_final: 0.7868 (mmm) REVERT: A 937 ASN cc_start: 0.7619 (m110) cc_final: 0.7284 (m-40) REVERT: A 968 LYS cc_start: 0.8579 (tmtt) cc_final: 0.7816 (mttt) REVERT: B 99 ARG cc_start: 0.7526 (mtt-85) cc_final: 0.7276 (mmt90) REVERT: B 224 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7218 (pp) REVERT: B 717 SER cc_start: 0.8940 (p) cc_final: 0.8055 (m) REVERT: B 796 LYS cc_start: 0.8028 (mttm) cc_final: 0.7765 (mptp) REVERT: B 968 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7549 (tmtt) REVERT: C 851 MET cc_start: 0.8476 (mtm) cc_final: 0.8258 (mtt) outliers start: 62 outliers final: 46 residues processed: 280 average time/residue: 0.3177 time to fit residues: 147.8075 Evaluate side-chains 262 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 213 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 0.0070 chunk 290 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24764 Z= 0.158 Angle : 0.510 7.074 33686 Z= 0.268 Chirality : 0.046 0.370 3952 Planarity : 0.004 0.085 4289 Dihedral : 6.106 58.713 4192 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 14.93 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2980 helix: 0.40 (0.21), residues: 654 sheet: -0.16 (0.20), residues: 625 loop : -1.21 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.002 0.001 HIS A 611 PHE 0.020 0.001 PHE B1079 TYR 0.020 0.001 TYR A1049 ARG 0.003 0.000 ARG A1089 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7023 (p90) REVERT: A 503 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 770 MET cc_start: 0.8389 (mmm) cc_final: 0.7762 (mmm) REVERT: A 937 ASN cc_start: 0.7410 (m110) cc_final: 0.7005 (m-40) REVERT: A 968 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7303 (mttt) REVERT: A 1020 LYS cc_start: 0.8544 (mttp) cc_final: 0.8188 (mttp) REVERT: B 224 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7095 (pp) REVERT: B 562 VAL cc_start: 0.8931 (p) cc_final: 0.8641 (t) REVERT: B 589 ASN cc_start: 0.8295 (p0) cc_final: 0.7987 (p0) REVERT: B 717 SER cc_start: 0.8630 (p) cc_final: 0.7923 (m) REVERT: B 968 LYS cc_start: 0.7474 (mtmt) cc_final: 0.6953 (tmtt) REVERT: C 421 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8617 (pt) REVERT: C 689 TYR cc_start: 0.8409 (t80) cc_final: 0.8169 (t80) REVERT: C 851 MET cc_start: 0.8367 (mtm) cc_final: 0.8161 (mtt) outliers start: 53 outliers final: 39 residues processed: 283 average time/residue: 0.3273 time to fit residues: 153.7061 Evaluate side-chains 274 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 231 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 180 optimal weight: 0.0050 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24764 Z= 0.176 Angle : 0.512 7.851 33686 Z= 0.267 Chirality : 0.046 0.358 3952 Planarity : 0.004 0.084 4289 Dihedral : 5.929 59.914 4192 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.06 % Allowed : 15.12 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 2980 helix: 0.56 (0.21), residues: 655 sheet: -0.06 (0.21), residues: 601 loop : -1.16 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 868 HIS 0.003 0.001 HIS A 611 PHE 0.030 0.001 PHE C 220 TYR 0.023 0.001 TYR A 200 ARG 0.004 0.000 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 242 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7042 (p90) REVERT: A 770 MET cc_start: 0.8389 (mmm) cc_final: 0.7792 (mmm) REVERT: A 937 ASN cc_start: 0.7615 (m110) cc_final: 0.7220 (m-40) REVERT: A 968 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7369 (mttt) REVERT: A 1020 LYS cc_start: 0.8518 (mttp) cc_final: 0.8200 (mttp) REVERT: B 224 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7071 (pp) REVERT: B 562 VAL cc_start: 0.8936 (p) cc_final: 0.8617 (t) REVERT: B 572 ASP cc_start: 0.8061 (m-30) cc_final: 0.7481 (m-30) REVERT: B 589 ASN cc_start: 0.8264 (p0) cc_final: 0.8040 (p0) REVERT: B 709 MET cc_start: 0.8823 (mtm) cc_final: 0.8437 (mtm) REVERT: B 717 SER cc_start: 0.8627 (p) cc_final: 0.7944 (m) REVERT: B 786 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8258 (mm110) REVERT: B 968 LYS cc_start: 0.7165 (mtmt) cc_final: 0.6772 (tmtt) REVERT: C 421 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8631 (pt) outliers start: 54 outliers final: 44 residues processed: 284 average time/residue: 0.3178 time to fit residues: 150.6274 Evaluate side-chains 281 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 183 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24764 Z= 0.162 Angle : 0.499 7.643 33686 Z= 0.261 Chirality : 0.046 0.358 3952 Planarity : 0.004 0.083 4289 Dihedral : 5.740 57.523 4192 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.13 % Allowed : 15.35 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 2980 helix: 0.73 (0.21), residues: 653 sheet: -0.03 (0.21), residues: 602 loop : -1.12 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 868 HIS 0.002 0.001 HIS B 611 PHE 0.024 0.001 PHE C 220 TYR 0.021 0.001 TYR A 200 ARG 0.004 0.000 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 249 time to evaluate : 2.630 Fit side-chains revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7062 (p90) REVERT: A 770 MET cc_start: 0.8369 (mmm) cc_final: 0.7780 (mmm) REVERT: A 937 ASN cc_start: 0.7537 (m110) cc_final: 0.7121 (m-40) REVERT: A 1020 LYS cc_start: 0.8511 (mttp) cc_final: 0.8185 (mttp) REVERT: B 562 VAL cc_start: 0.8907 (p) cc_final: 0.8621 (t) REVERT: B 572 ASP cc_start: 0.8028 (m-30) cc_final: 0.7472 (m-30) REVERT: B 709 MET cc_start: 0.8815 (mtm) cc_final: 0.8426 (mtm) REVERT: B 717 SER cc_start: 0.8538 (p) cc_final: 0.7990 (m) REVERT: B 968 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6641 (tmtt) REVERT: C 421 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8591 (pt) outliers start: 56 outliers final: 46 residues processed: 291 average time/residue: 0.3330 time to fit residues: 161.1754 Evaluate side-chains 290 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 242 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 269 optimal weight: 0.5980 chunk 276 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 0.0470 overall best weight: 0.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24764 Z= 0.162 Angle : 0.498 8.080 33686 Z= 0.260 Chirality : 0.046 0.337 3952 Planarity : 0.004 0.082 4289 Dihedral : 5.646 57.038 4192 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.06 % Allowed : 15.73 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2980 helix: 0.84 (0.21), residues: 653 sheet: 0.01 (0.21), residues: 602 loop : -1.10 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 868 HIS 0.002 0.001 HIS B 611 PHE 0.038 0.001 PHE B1079 TYR 0.020 0.001 TYR A 200 ARG 0.003 0.000 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 248 time to evaluate : 2.860 Fit side-chains revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7022 (p90) REVERT: A 503 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 770 MET cc_start: 0.8461 (mmm) cc_final: 0.7847 (mmm) REVERT: A 796 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7554 (mttm) REVERT: A 937 ASN cc_start: 0.7521 (m110) cc_final: 0.7106 (m-40) REVERT: A 1006 LEU cc_start: 0.8550 (tp) cc_final: 0.8182 (tp) REVERT: A 1020 LYS cc_start: 0.8562 (mttp) cc_final: 0.8232 (mttp) REVERT: B 562 VAL cc_start: 0.8913 (p) cc_final: 0.8650 (t) REVERT: B 572 ASP cc_start: 0.8007 (m-30) cc_final: 0.7442 (m-30) REVERT: B 709 MET cc_start: 0.8818 (mtm) cc_final: 0.8411 (mtm) REVERT: B 717 SER cc_start: 0.8589 (p) cc_final: 0.8080 (m) REVERT: B 968 LYS cc_start: 0.7132 (mtmt) cc_final: 0.6657 (tmtt) REVERT: C 421 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8582 (pt) REVERT: C 772 LYS cc_start: 0.7882 (ptmm) cc_final: 0.7627 (pttp) outliers start: 54 outliers final: 47 residues processed: 288 average time/residue: 0.3126 time to fit residues: 149.4939 Evaluate side-chains 292 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 242 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 298 optimal weight: 0.6980 chunk 275 optimal weight: 7.9990 chunk 237 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24764 Z= 0.158 Angle : 0.494 7.817 33686 Z= 0.258 Chirality : 0.046 0.342 3952 Planarity : 0.004 0.081 4289 Dihedral : 5.566 56.592 4192 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.09 % Allowed : 15.92 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 2980 helix: 0.94 (0.22), residues: 653 sheet: 0.01 (0.21), residues: 604 loop : -1.07 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 101 HIS 0.002 0.001 HIS B 611 PHE 0.024 0.001 PHE C 220 TYR 0.022 0.001 TYR B 200 ARG 0.003 0.000 ARG C1089 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7056 (p90) REVERT: A 503 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 770 MET cc_start: 0.8450 (mmm) cc_final: 0.7873 (mmm) REVERT: A 796 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7555 (mttm) REVERT: A 937 ASN cc_start: 0.7473 (m110) cc_final: 0.7120 (m-40) REVERT: A 1006 LEU cc_start: 0.8543 (tp) cc_final: 0.8189 (tp) REVERT: A 1020 LYS cc_start: 0.8558 (mttp) cc_final: 0.8218 (mttp) REVERT: B 163 TYR cc_start: 0.8075 (t80) cc_final: 0.7807 (t80) REVERT: B 562 VAL cc_start: 0.8900 (p) cc_final: 0.8645 (t) REVERT: B 572 ASP cc_start: 0.8070 (m-30) cc_final: 0.7561 (m-30) REVERT: B 589 ASN cc_start: 0.8502 (p0) cc_final: 0.8237 (p0) REVERT: B 709 MET cc_start: 0.8819 (mtm) cc_final: 0.8400 (mtm) REVERT: B 717 SER cc_start: 0.8563 (p) cc_final: 0.8073 (m) REVERT: B 968 LYS cc_start: 0.6593 (mtmt) cc_final: 0.6277 (tmtt) REVERT: C 421 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8560 (pt) outliers start: 55 outliers final: 52 residues processed: 295 average time/residue: 0.3309 time to fit residues: 161.7227 Evaluate side-chains 301 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 889 ASN Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.121226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.095965 restraints weight = 28219.456| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.84 r_work: 0.2702 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24764 Z= 0.195 Angle : 0.512 7.420 33686 Z= 0.267 Chirality : 0.046 0.333 3952 Planarity : 0.004 0.082 4289 Dihedral : 5.614 56.327 4192 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.21 % Allowed : 15.88 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 2980 helix: 0.89 (0.21), residues: 653 sheet: 0.07 (0.21), residues: 612 loop : -1.12 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS B 611 PHE 0.034 0.001 PHE B1079 TYR 0.020 0.001 TYR A1049 ARG 0.003 0.000 ARG C1089 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.78 seconds wall clock time: 80 minutes 4.48 seconds (4804.48 seconds total)