Starting phenix.real_space_refine (version: dev) on Sat Feb 25 00:59:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2023/8h12_34422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2023/8h12_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_2023/8h12_34422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2023/8h12_34422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2023/8h12_34422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h12_34422/02_2023/8h12_34422.pdb" } resolution = 3.44681 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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 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 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 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 chiralities: 13 Time building chain proxies: 13.20, per 1000 atoms: 0.54 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: 10.17 Conformation dependent library (CDL) restraints added in 3.4 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: 1.99 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: 10.10 Time building geometry restraints manager: 10.91 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=" 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=" CB CYS A 969 " pdb=" SG CYS A 969 " ideal model delta sigma weight residual 1.808 1.741 0.067 3.30e-02 9.18e+02 4.10e+00 bond pdb=" CB VAL B1047 " pdb=" CG1 VAL B1047 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.65e+00 bond pdb=" CB VAL C1047 " pdb=" CG1 VAL C1047 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.62e+00 bond pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " ideal model delta sigma weight residual 1.808 1.860 -0.052 3.30e-02 9.18e+02 2.47e+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: 13318 17.86 - 35.72: 1109 35.72 - 53.58: 191 53.58 - 71.45: 33 71.45 - 89.31: 27 Dihedral angle restraints: 14678 sinusoidal: 5864 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 14675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3375 0.078 - 0.155: 538 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 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. 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: 1.040 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: 5.560 Check model and map are aligned: 0.370 Process input model: 63.530 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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= 0.378 Angle : 0.784 12.567 33686 Z= 0.434 Chirality : 0.056 0.388 3952 Planarity : 0.006 0.116 4289 Dihedral : 13.746 89.307 8880 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 % 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 *********************** 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 : 3.450 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3448 time to fit residues: 154.3224 Evaluate side-chains 216 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9746 ------------------------------------------------------------------------------- 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 B 937 ASN B1088 GLN C 301 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0794 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= 0.373 Angle : 0.629 9.172 33686 Z= 0.336 Chirality : 0.050 0.374 3952 Planarity : 0.005 0.102 4289 Dihedral : 5.256 24.743 3517 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.95 % 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: -1.12 (0.19), residues: 679 sheet: -0.21 (0.21), residues: 610 loop : -1.40 (0.13), residues: 1691 *********************** 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 258 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 2.625 Fit side-chains outliers start: 25 outliers final: 21 residues processed: 247 average time/residue: 0.3455 time to fit residues: 141.4429 Evaluate side-chains 232 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2295 time to fit residues: 13.0935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 185 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24764 Z= 0.239 Angle : 0.546 7.503 33686 Z= 0.292 Chirality : 0.047 0.345 3952 Planarity : 0.005 0.094 4289 Dihedral : 4.904 21.337 3517 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.65 % 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: -1.28 (0.14), residues: 2980 helix: -0.35 (0.20), residues: 666 sheet: -0.16 (0.21), residues: 611 loop : -1.33 (0.13), residues: 1703 *********************** 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 264 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 247 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 259 average time/residue: 0.3389 time to fit residues: 146.6571 Evaluate side-chains 234 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 2.916 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2349 time to fit residues: 10.1265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24764 Z= 0.187 Angle : 0.512 8.249 33686 Z= 0.273 Chirality : 0.046 0.342 3952 Planarity : 0.004 0.090 4289 Dihedral : 4.686 20.903 3517 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.22 % 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: -1.02 (0.14), residues: 2980 helix: 0.19 (0.21), residues: 654 sheet: -0.18 (0.20), residues: 629 loop : -1.23 (0.13), residues: 1697 *********************** 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 271 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 2.833 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 260 average time/residue: 0.3371 time to fit residues: 144.7725 Evaluate side-chains 243 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2154 time to fit residues: 10.1292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 215 optimal weight: 3.9990 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: 0.9990 chunk 73 optimal weight: 3.9990 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 904 GLN B 201 GLN B 301 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 24764 Z= 0.372 Angle : 0.603 7.593 33686 Z= 0.320 Chirality : 0.050 0.455 3952 Planarity : 0.005 0.086 4289 Dihedral : 4.923 23.070 3517 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 1.26 % 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: -1.19 (0.14), residues: 2980 helix: -0.11 (0.20), residues: 669 sheet: -0.16 (0.21), residues: 612 loop : -1.33 (0.13), residues: 1699 *********************** 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 270 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 263 average time/residue: 0.3399 time to fit residues: 149.6698 Evaluate side-chains 242 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 2.886 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2393 time to fit residues: 14.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 290 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 134 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 24764 Z= 0.179 Angle : 0.512 7.273 33686 Z= 0.273 Chirality : 0.046 0.352 3952 Planarity : 0.004 0.085 4289 Dihedral : 4.669 21.276 3517 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.76 % 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: 0.36 (0.21), residues: 655 sheet: -0.07 (0.21), residues: 613 loop : -1.23 (0.14), residues: 1712 *********************** 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 261 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 257 average time/residue: 0.3375 time to fit residues: 145.3171 Evaluate side-chains 236 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 225 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2403 time to fit residues: 8.8242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 165 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 180 optimal weight: 0.0010 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1451 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= 0.149 Angle : 0.491 7.568 33686 Z= 0.261 Chirality : 0.045 0.317 3952 Planarity : 0.004 0.084 4289 Dihedral : 4.485 20.335 3517 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.95 % 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: 0.70 (0.22), residues: 652 sheet: 0.00 (0.21), residues: 605 loop : -1.12 (0.14), residues: 1723 *********************** 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 281 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 276 average time/residue: 0.3330 time to fit residues: 154.5204 Evaluate side-chains 248 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2525 time to fit residues: 10.7702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 172 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8369 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24764 Z= 0.207 Angle : 0.517 7.822 33686 Z= 0.273 Chirality : 0.046 0.322 3952 Planarity : 0.004 0.082 4289 Dihedral : 4.515 18.546 3517 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.46 % 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: -0.71 (0.15), residues: 2980 helix: 0.67 (0.21), residues: 653 sheet: -0.00 (0.21), residues: 609 loop : -1.12 (0.14), residues: 1718 *********************** 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 256 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 252 average time/residue: 0.3403 time to fit residues: 142.9945 Evaluate side-chains 248 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 2.808 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2497 time to fit residues: 9.3190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24764 Z= 0.199 Angle : 0.511 7.695 33686 Z= 0.271 Chirality : 0.046 0.317 3952 Planarity : 0.004 0.082 4289 Dihedral : 4.495 17.857 3517 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.42 % 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: -0.68 (0.15), residues: 2980 helix: 0.74 (0.21), residues: 653 sheet: -0.01 (0.21), residues: 609 loop : -1.11 (0.14), residues: 1718 *********************** 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 255 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 252 average time/residue: 0.3659 time to fit residues: 152.8061 Evaluate side-chains 240 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 231 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2385 time to fit residues: 7.9882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 chunk 275 optimal weight: 0.0040 chunk 237 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 183 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.8398 ------------------------------------------------------------------------------- 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** B1088 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 24764 Z= 0.317 Angle : 0.577 9.392 33686 Z= 0.305 Chirality : 0.048 0.316 3952 Planarity : 0.005 0.081 4289 Dihedral : 4.711 19.606 3517 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.30 % 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: -0.87 (0.15), residues: 2980 helix: 0.50 (0.21), residues: 653 sheet: -0.11 (0.21), residues: 611 loop : -1.20 (0.14), residues: 1716 ********************** 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 238 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 230 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 237 average time/residue: 0.3419 time to fit residues: 135.9552 Evaluate side-chains 229 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 224 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2218 time to fit residues: 6.0583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 2.9990 chunk 253 optimal weight: 0.0470 chunk 72 optimal weight: 0.0570 chunk 219 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 238 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.122112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.096244 restraints weight = 28131.333| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.84 r_work: 0.2748 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 24764 Z= 0.142 Angle : 0.493 7.600 33686 Z= 0.262 Chirality : 0.045 0.408 3952 Planarity : 0.004 0.081 4289 Dihedral : 4.450 16.883 3517 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.27 % 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: -0.63 (0.15), residues: 2980 helix: 0.87 (0.22), residues: 652 sheet: -0.02 (0.21), residues: 603 loop : -1.09 (0.14), residues: 1725 =============================================================================== Job complete usr+sys time: 4389.83 seconds wall clock time: 81 minutes 45.70 seconds (4905.70 seconds total)