Starting phenix.real_space_refine (version: dev) on Mon Feb 27 23:12:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cai_30332/02_2023/7cai_30332.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cai_30332/02_2023/7cai_30332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cai_30332/02_2023/7cai_30332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cai_30332/02_2023/7cai_30332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cai_30332/02_2023/7cai_30332.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cai_30332/02_2023/7cai_30332.pdb" } resolution = 3.49 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= 0.001 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 ARG 34": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" 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: 31266 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7993 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 7995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7995 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8000 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1635 Chain: "E" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1635 Chain: "G" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER D 114 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER D 114 " occ=0.48 residue: pdb=" N ASER F 114 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER F 114 " occ=0.48 Time building chain proxies: 18.40, per 1000 atoms: 0.59 Number of scatterers: 31266 At special positions: 0 Unit cell: (196.56, 171.6, 190.32, 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 126 16.00 O 6157 8.00 N 5094 7.00 C 19889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.02 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=1, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 5.6 seconds 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7342 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 78 sheets defined 18.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.704A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.787A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 746 through 757 removed outlier: 4.238A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 772 removed outlier: 3.577A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 783 removed outlier: 3.632A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.550A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.588A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.032A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.526A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.568A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.867A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.148A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.945A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.951A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.542A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.552A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.687A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.516A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.591A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 4.262A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.505A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.631A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.587A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.655A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.116A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 4.077A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.030A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 370' Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.584A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.514A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.518A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.265A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 removed outlier: 4.475A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.630A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.594A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 903 through 908 removed outlier: 3.810A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.932A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.633A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.489A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.344A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1146' Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.798A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.916A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.682A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.697A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 4.184A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.549A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.291A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.540A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.506A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.843A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.566A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.566A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AC5, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AC6, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.851A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 313 through 317 removed outlier: 5.231A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.597A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.995A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.225A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.225A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.196A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.165A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 735 removed outlier: 3.836A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.566A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.696A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.055A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.055A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.577A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.098A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 311 through 318 removed outlier: 4.422A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF3, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.210A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.210A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 576 through 577 Processing sheet with id=AF7, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.570A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 720 removed outlier: 6.212A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 723 through 728 removed outlier: 3.703A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG4, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AG5, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.170A pdb=" N VAL D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.631A pdb=" N GLN D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 104 " --> pdb=" O GLN D 10 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AG8, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AG9, first strand: chain 'D' and resid 116 through 118 Processing sheet with id=AH1, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.921A pdb=" N TYR D 191 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE D 206 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 204 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.950A pdb=" N GLU E 82 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.122A pdb=" N GLU E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.700A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 191 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU E 145 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 189 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER E 184 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA E 175 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 186 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.947A pdb=" N THR E 158 " --> pdb=" O ASN E 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 206 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS E 203 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS E 216 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 205 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL E 214 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.170A pdb=" N VAL F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.631A pdb=" N GLN F 10 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 104 " --> pdb=" O GLN F 10 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=AH9, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AI1, first strand: chain 'F' and resid 116 through 118 Processing sheet with id=AI2, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.920A pdb=" N TYR F 191 " --> pdb=" O PHE F 206 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 206 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS F 204 " --> pdb=" O CYS F 193 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.950A pdb=" N GLU G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.122A pdb=" N GLU G 10 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR G 50 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER G 59 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.700A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 191 " --> pdb=" O ALA G 143 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU G 145 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 189 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER G 184 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA G 175 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 186 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 188 " --> pdb=" O HIS G 171 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.948A pdb=" N THR G 158 " --> pdb=" O ASN G 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN G 206 " --> pdb=" O THR G 158 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS G 203 " --> pdb=" O LYS G 216 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS G 216 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL G 205 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL G 214 " --> pdb=" O VAL G 205 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2436 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: 14.63 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9360 1.33 - 1.46: 8328 1.46 - 1.59: 14136 1.59 - 1.71: 0 1.71 - 1.84: 157 Bond restraints: 31981 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.580 -0.246 2.34e-02 1.83e+03 1.10e+02 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.331 1.441 -0.110 1.63e-02 3.76e+03 4.55e+01 bond pdb=" C ILE C 805 " pdb=" N LEU C 806 " ideal model delta sigma weight residual 1.331 1.234 0.097 2.07e-02 2.33e+03 2.21e+01 bond pdb=" C ILE A 805 " pdb=" N LEU A 806 " ideal model delta sigma weight residual 1.331 1.263 0.068 2.07e-02 2.33e+03 1.08e+01 bond pdb=" C ILE C 587 " pdb=" N THR C 588 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.05e+01 ... (remaining 31976 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.96: 698 104.96 - 113.06: 17931 113.06 - 121.15: 16225 121.15 - 129.25: 8517 129.25 - 137.35: 158 Bond angle restraints: 43529 Sorted by residual: angle pdb=" C TRP B 152 " pdb=" CA TRP B 152 " pdb=" CB TRP B 152 " ideal model delta sigma weight residual 115.79 108.21 7.58 1.19e+00 7.06e-01 4.06e+01 angle pdb=" C VAL B 159 " pdb=" N TYR B 160 " pdb=" CA TYR B 160 " ideal model delta sigma weight residual 122.84 112.21 10.63 1.81e+00 3.05e-01 3.45e+01 angle pdb=" C LEU B 335 " pdb=" N CYS B 336 " pdb=" CA CYS B 336 " ideal model delta sigma weight residual 121.61 129.36 -7.75 1.39e+00 5.18e-01 3.11e+01 angle pdb=" N HIS B 66 " pdb=" CA HIS B 66 " pdb=" C HIS B 66 " ideal model delta sigma weight residual 108.24 115.45 -7.21 1.32e+00 5.74e-01 2.99e+01 angle pdb=" C VAL B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 123.96 116.82 7.14 1.44e+00 4.82e-01 2.46e+01 ... (remaining 43524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 18132 17.51 - 35.02: 637 35.02 - 52.53: 86 52.53 - 70.03: 35 70.03 - 87.54: 15 Dihedral angle restraints: 18905 sinusoidal: 7496 harmonic: 11409 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.16 87.16 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA VAL B 159 " pdb=" C VAL B 159 " pdb=" N TYR B 160 " pdb=" CA TYR B 160 " ideal model delta harmonic sigma weight residual -180.00 -133.49 -46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 135.58 44.42 0 5.00e+00 4.00e-02 7.89e+01 ... (remaining 18902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 5076 0.175 - 0.349: 28 0.349 - 0.524: 4 0.524 - 0.699: 2 0.699 - 0.873: 1 Chirality restraints: 5111 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.99e+00 ... (remaining 5108 not shown) Planarity restraints: 5575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " 0.033 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" CG TRP B 64 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " 0.033 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP C 64 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 800 " 0.018 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE A 800 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 800 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 800 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 800 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 800 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 800 " -0.000 2.00e-02 2.50e+03 ... (remaining 5572 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 36 2.14 - 2.83: 10828 2.83 - 3.52: 44619 3.52 - 4.21: 77236 4.21 - 4.90: 129080 Nonbonded interactions: 261799 Sorted by model distance: nonbonded pdb=" CZ PHE B 559 " pdb=" O PHE B 565 " model vdw 1.448 3.340 nonbonded pdb=" CB PHE A 43 " pdb=" OE1 GLN B 563 " model vdw 1.528 3.440 nonbonded pdb=" CA PHE A 43 " pdb=" OE1 GLN B 563 " model vdw 1.602 3.470 nonbonded pdb=" CB LEU A 560 " pdb=" OE1 GLN A 563 " model vdw 1.739 3.440 nonbonded pdb=" O ASN A 856 " pdb=" N LEU A 858 " model vdw 1.739 2.520 ... (remaining 261794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 524 or (resid 525 and (name N o \ r name CA or name C or name O or name CB )) or resid 526 through 1147 or resid 1 \ 301 through 1310)) selection = (chain 'B' and (resid 25 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 1147 or resid 1301 through 1310 \ )) selection = (chain 'C' and (resid 25 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 524 or (resid 525 and (name N o \ r name CA or name C or name O or name CB )) or resid 526 through 527 or (resid 5 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 529 through \ 698 or (resid 699 and (name N or name CA or name C or name O or name CB )) or r \ esid 700 through 1147 or resid 1301 through 1310)) } ncs_group { reference = (chain 'D' and (resid 2 through 113 or resid 115 through 208)) selection = (chain 'F' and (resid 2 through 113 or resid 115 through 208)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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 126 5.16 5 C 19889 2.51 5 N 5094 2.21 5 O 6157 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.040 Extract box with map and model: 16.360 Check model and map are aligned: 0.440 Process input model: 86.450 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.290 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 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 : 0.012 0.246 31981 Z= 0.761 Angle : 1.062 15.758 43529 Z= 0.582 Chirality : 0.062 0.873 5111 Planarity : 0.006 0.072 5530 Dihedral : 10.064 87.542 11440 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.27 % Favored : 90.55 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.39 (0.10), residues: 3857 helix: -4.35 (0.10), residues: 661 sheet: -2.76 (0.13), residues: 922 loop : -2.56 (0.10), residues: 2274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 318 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 339 average time/residue: 0.4961 time to fit residues: 261.0297 Evaluate side-chains 165 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 3.236 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.3480 time to fit residues: 14.7608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.9990 chunk 294 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 100 optimal weight: 0.0970 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 352 optimal weight: 30.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 317 ASN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 439 ASN A 655 HIS A 658 ASN A 784 GLN A 856 ASN A 901 GLN A 913 GLN A1088 HIS B 81 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN C 239 GLN C 245 HIS C 317 ASN C 437 ASN C 580 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1011 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN D 10 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 188 HIS E 31 ASN F 10 GLN ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN F 188 HIS G 31 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 31981 Z= 0.245 Angle : 0.758 13.238 43529 Z= 0.402 Chirality : 0.051 0.828 5111 Planarity : 0.005 0.087 5530 Dihedral : 7.396 41.710 4536 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.11), residues: 3857 helix: -2.45 (0.15), residues: 701 sheet: -2.42 (0.14), residues: 914 loop : -1.98 (0.11), residues: 2242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 222 average time/residue: 0.4431 time to fit residues: 164.0775 Evaluate side-chains 167 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 3.587 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3146 time to fit residues: 14.5700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 239 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 381 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 218 GLN B 239 GLN B 784 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 137 ASN C 207 HIS C 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 31981 Z= 0.338 Angle : 0.696 12.258 43529 Z= 0.368 Chirality : 0.050 0.776 5111 Planarity : 0.005 0.078 5530 Dihedral : 6.864 39.385 4536 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.92 % Favored : 93.90 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.74 (0.12), residues: 3857 helix: -1.18 (0.18), residues: 694 sheet: -2.27 (0.15), residues: 971 loop : -1.79 (0.12), residues: 2192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 161 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 20 residues processed: 202 average time/residue: 0.4385 time to fit residues: 146.8154 Evaluate side-chains 164 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 3.488 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2879 time to fit residues: 15.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 0.0770 chunk 265 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 354 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN C 81 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 31981 Z= 0.245 Angle : 0.633 11.092 43529 Z= 0.334 Chirality : 0.047 0.752 5111 Planarity : 0.004 0.069 5530 Dihedral : 6.402 35.776 4536 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.26 (0.13), residues: 3857 helix: -0.39 (0.20), residues: 697 sheet: -2.10 (0.15), residues: 943 loop : -1.57 (0.13), residues: 2217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 181 average time/residue: 0.4675 time to fit residues: 142.6823 Evaluate side-chains 145 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 3.155 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3000 time to fit residues: 9.9844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 279 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 336 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 360 ASN A 439 ASN A 498 GLN A 762 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 121 ASN B 239 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN G 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 31981 Z= 0.421 Angle : 0.707 12.927 43529 Z= 0.370 Chirality : 0.049 0.667 5111 Planarity : 0.005 0.059 5530 Dihedral : 6.507 36.220 4536 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.55 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.33 (0.13), residues: 3857 helix: -0.40 (0.20), residues: 699 sheet: -2.05 (0.15), residues: 964 loop : -1.69 (0.13), residues: 2194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 150 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 27 residues processed: 203 average time/residue: 0.4355 time to fit residues: 151.5423 Evaluate side-chains 168 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 3.447 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3063 time to fit residues: 20.8722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 375 optimal weight: 10.0000 chunk 311 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 498 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 81 ASN B 218 GLN C 81 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN E 31 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 31981 Z= 0.205 Angle : 0.605 11.779 43529 Z= 0.318 Chirality : 0.046 0.665 5111 Planarity : 0.004 0.050 5530 Dihedral : 6.125 36.089 4536 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.38 % Favored : 94.44 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.02 (0.13), residues: 3857 helix: -0.03 (0.20), residues: 706 sheet: -1.88 (0.16), residues: 950 loop : -1.51 (0.13), residues: 2201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 7 residues processed: 177 average time/residue: 0.4409 time to fit residues: 130.8921 Evaluate side-chains 148 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3300 time to fit residues: 9.0992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 316 optimal weight: 30.0000 chunk 209 optimal weight: 0.0770 chunk 373 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 172 optimal weight: 0.0170 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 31981 Z= 0.268 Angle : 0.612 11.003 43529 Z= 0.321 Chirality : 0.046 0.630 5111 Planarity : 0.004 0.045 5530 Dihedral : 6.002 34.186 4536 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.39 % Favored : 93.43 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3857 helix: 0.07 (0.20), residues: 700 sheet: -1.82 (0.16), residues: 942 loop : -1.50 (0.13), residues: 2215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 170 average time/residue: 0.4189 time to fit residues: 122.8861 Evaluate side-chains 148 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 3.891 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3518 time to fit residues: 12.0122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 112 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 293 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 481 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 31981 Z= 0.221 Angle : 0.590 10.152 43529 Z= 0.309 Chirality : 0.046 0.623 5111 Planarity : 0.004 0.049 5530 Dihedral : 5.808 32.179 4536 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3857 helix: 0.29 (0.20), residues: 688 sheet: -1.72 (0.16), residues: 941 loop : -1.41 (0.13), residues: 2228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.4321 time to fit residues: 116.3040 Evaluate side-chains 142 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 3.689 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3128 time to fit residues: 9.0839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 1.9990 chunk 358 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 348 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 151 optimal weight: 0.0370 chunk 273 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 chunk 314 optimal weight: 30.0000 chunk 329 optimal weight: 0.8980 chunk 347 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 31981 Z= 0.187 Angle : 0.574 9.408 43529 Z= 0.301 Chirality : 0.045 0.617 5111 Planarity : 0.004 0.049 5530 Dihedral : 5.593 28.235 4536 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.32 % Favored : 94.52 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -1.61 (0.13), residues: 3857 helix: 0.48 (0.20), residues: 697 sheet: -1.55 (0.16), residues: 923 loop : -1.35 (0.13), residues: 2237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 152 average time/residue: 0.4517 time to fit residues: 116.0217 Evaluate side-chains 138 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2999 time to fit residues: 5.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 386 optimal weight: 30.0000 chunk 355 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 31981 Z= 0.224 Angle : 0.584 9.653 43529 Z= 0.304 Chirality : 0.045 0.604 5111 Planarity : 0.004 0.049 5530 Dihedral : 5.562 25.024 4536 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.74 % Favored : 94.11 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -1.59 (0.13), residues: 3857 helix: 0.49 (0.20), residues: 697 sheet: -1.50 (0.16), residues: 924 loop : -1.35 (0.13), residues: 2236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.4603 time to fit residues: 109.5707 Evaluate side-chains 144 residues out of total 3425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3322 time to fit residues: 9.6764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.5980 chunk 327 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 308 optimal weight: 0.0270 chunk 129 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 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 = 0.4339 r_free = 0.4339 target = 0.132542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.096841 restraints weight = 137435.963| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 5.62 r_work: 0.3327 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4339 r_free = 0.4339 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4339 r_free = 0.4339 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 31981 Z= 0.271 Angle : 0.602 9.272 43529 Z= 0.314 Chirality : 0.046 0.589 5111 Planarity : 0.004 0.048 5530 Dihedral : 5.619 28.243 4536 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.61 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -1.62 (0.13), residues: 3857 helix: 0.42 (0.20), residues: 698 sheet: -1.52 (0.16), residues: 931 loop : -1.36 (0.13), residues: 2228 =============================================================================== Job complete usr+sys time: 5483.82 seconds wall clock time: 102 minutes 47.46 seconds (6167.46 seconds total)