Starting phenix.real_space_refine on Sun Aug 24 02:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua9_63982/08_2025/9ua9_63982.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua9_63982/08_2025/9ua9_63982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ua9_63982/08_2025/9ua9_63982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua9_63982/08_2025/9ua9_63982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ua9_63982/08_2025/9ua9_63982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua9_63982/08_2025/9ua9_63982.map" } resolution = 1.99 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9957 2.51 5 N 2601 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16357 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "H" Number of atoms: 974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} bond proxies already assigned to first conformer: 986 Chain: "A" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "C" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "B" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "G" Number of atoms: 974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} bond proxies already assigned to first conformer: 986 Chain: "I" Number of atoms: 974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} bond proxies already assigned to first conformer: 986 Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 153 Classifications: {'water': 153} Link IDs: {None: 152} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AASN H 70 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN H 70 " occ=0.50 residue: pdb=" N AASN A 155 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 155 " occ=0.50 residue: pdb=" N AASN A 350 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 350 " occ=0.50 residue: pdb=" N ASER A 461 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 461 " occ=0.50 residue: pdb=" N AASN C 155 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 155 " occ=0.50 residue: pdb=" N AASN C 350 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 350 " occ=0.50 residue: pdb=" N ASER C 461 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 461 " occ=0.50 residue: pdb=" N AASN B 155 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 155 " occ=0.50 residue: pdb=" N AASN B 350 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 350 " occ=0.50 residue: pdb=" N ASER B 461 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 461 " occ=0.50 residue: pdb=" N AASN G 70 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN G 70 " occ=0.50 residue: pdb=" N AASN I 70 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN I 70 " occ=0.50 Time building chain proxies: 6.67, per 1000 atoms: 0.41 Number of scatterers: 16357 At special positions: 0 Unit cell: (125.06, 123.58, 142.08, 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 75 16.00 O 3724 8.00 N 2601 7.00 C 9957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 501 " - " ASN A 99 " " NAG A 502 " - " ASN A 67 " " NAG A 503 " - " ASN A 464 " " NAG B 501 " - " ASN B 99 " " NAG B 502 " - " ASN B 67 " " NAG B 503 " - " ASN B 464 " " NAG C 501 " - " ASN C 99 " " NAG C 502 " - " ASN C 67 " " NAG C 503 " - " ASN C 464 " " NAG J 1 " - " ASN A 414 " " NAG K 1 " - " ASN C 414 " " NAG L 1 " - " ASN B 414 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 36 sheets defined 30.5% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.524A pdb=" N ASP F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.938A pdb=" N TYR H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.733A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.677A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.987A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.620A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.561A pdb=" N MET A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.574A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.746A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.575A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 476 removed outlier: 3.632A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 475 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.653A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.970A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 Proline residue: C 89 - end of helix removed outlier: 3.596A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 4.586A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 191 through 215 removed outlier: 4.574A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.772A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 441 removed outlier: 3.634A pdb=" N GLU C 441 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 476 removed outlier: 3.621A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 475 " --> pdb=" O LYS C 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.647A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.953A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 3.584A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.379A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.653A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.707A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.595A pdb=" N GLU B 441 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 476 removed outlier: 3.636A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 475 " --> pdb=" O LYS B 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.901A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.680A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.870A pdb=" N TYR I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.536A pdb=" N ASP E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.566A pdb=" N ASP D 83 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.461A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU F 110 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLU F 12 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.461A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU F 110 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLU F 12 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.013A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 101 through 103 Processing sheet with id=AA8, first strand: chain 'A' and resid 158 through 162 removed outlier: 12.755A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.338A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.791A pdb=" N MET A 115 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AB3, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB4, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AB6, first strand: chain 'C' and resid 158 through 162 removed outlier: 12.784A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 263 through 270 removed outlier: 3.523A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE C 284 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN C 51 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR C 286 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS C 49 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 392 through 394 removed outlier: 6.858A pdb=" N ILE C 426 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 158 through 162 removed outlier: 12.755A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.319A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.602A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.028A pdb=" N VAL G 115 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 101 through 103 Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.603A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.063A pdb=" N VAL I 115 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AD4, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.432A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU E 12 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.432A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU E 12 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 98 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD7, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.463A pdb=" N ALA D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU D 110 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU D 12 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.463A pdb=" N ALA D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU D 110 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU D 12 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 18 through 23 716 hydrogen bonds defined for protein. 1830 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: 3.16 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5097 1.35 - 1.46: 3653 1.46 - 1.58: 7231 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 16089 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 16084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 21032 1.26 - 2.53: 702 2.53 - 3.79: 128 3.79 - 5.05: 23 5.05 - 6.32: 6 Bond angle restraints: 21891 Sorted by residual: angle pdb=" C TYR F 51 " pdb=" N ASN F 52 " pdb=" CA ASN F 52 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C TYR E 51 " pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.93e+00 angle pdb=" C TYR D 51 " pdb=" N ASN D 52 " pdb=" CA ASN D 52 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.10e+00 angle pdb=" C ILE C 187 " pdb=" N ASP C 188 " pdb=" CA ASP C 188 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" CA CYS C 192 " pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " ideal model delta sigma weight residual 114.40 119.34 -4.94 2.30e+00 1.89e-01 4.61e+00 ... (remaining 21886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9497 17.65 - 35.31: 349 35.31 - 52.96: 81 52.96 - 70.62: 33 70.62 - 88.27: 3 Dihedral angle restraints: 9963 sinusoidal: 4017 harmonic: 5946 Sorted by residual: dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -124.20 38.20 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -124.12 38.12 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CA ILE A 288 " pdb=" C ILE A 288 " pdb=" N GLN A 289 " pdb=" CA GLN A 289 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1478 0.030 - 0.060: 667 0.060 - 0.090: 235 0.090 - 0.120: 199 0.120 - 0.150: 46 Chirality restraints: 2625 Sorted by residual: chirality pdb=" CA VAL C 269 " pdb=" N VAL C 269 " pdb=" C VAL C 269 " pdb=" CB VAL C 269 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA VAL A 269 " pdb=" N VAL A 269 " pdb=" C VAL A 269 " pdb=" CB VAL A 269 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA VAL B 312 " pdb=" N VAL B 312 " pdb=" C VAL B 312 " pdb=" CB VAL B 312 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 2622 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 215 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 216 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 215 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 216 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 215 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO C 216 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.017 5.00e-02 4.00e+02 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 593 2.72 - 3.27: 16261 3.27 - 3.81: 26711 3.81 - 4.36: 35311 4.36 - 4.90: 57187 Nonbonded interactions: 136063 Sorted by model distance: nonbonded pdb=" OE1 GLU B 95 " pdb=" O HOH B 601 " model vdw 2.177 3.040 nonbonded pdb=" O HOH B 601 " pdb=" O HOH B 693 " model vdw 2.189 3.040 nonbonded pdb=" O HOH B 643 " pdb=" O HOH B 736 " model vdw 2.215 3.040 nonbonded pdb=" O GLY B 73 " pdb=" O HOH B 602 " model vdw 2.297 3.040 nonbonded pdb=" O HOH B 730 " pdb=" O HOH B 736 " model vdw 2.298 3.040 ... (remaining 136058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 154 or resid 156 through 349 or resid 351 throu \ gh 460 or resid 462 through 503)) selection = (chain 'B' and (resid 27 through 154 or resid 156 through 349 or resid 351 throu \ gh 460 or resid 462 through 503)) selection = (chain 'C' and (resid 27 through 154 or resid 156 through 349 or resid 351 throu \ gh 460 or resid 462 through 503)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 1 through 69 or resid 71 through 125)) selection = (chain 'H' and (resid 1 through 69 or resid 71 through 125)) selection = (chain 'I' and (resid 1 through 69 or resid 71 through 125)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 10.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.330 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.003 0.039 16123 Z= 0.157 Angle : 0.574 6.317 21974 Z= 0.308 Chirality : 0.047 0.150 2625 Planarity : 0.004 0.035 2766 Dihedral : 10.731 88.274 6096 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2043 helix: 2.34 (0.25), residues: 447 sheet: 0.89 (0.21), residues: 594 loop : -0.51 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 67 TYR 0.012 0.001 TYR A 438 PHE 0.012 0.002 PHE G 113 TRP 0.010 0.001 TRP I 33 HIS 0.005 0.001 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00289 (16089) covalent geometry : angle 0.56696 (21891) SS BOND : bond 0.00617 ( 19) SS BOND : angle 1.16554 ( 38) hydrogen bonds : bond 0.13055 ( 695) hydrogen bonds : angle 5.71519 ( 1830) link_BETA1-4 : bond 0.00667 ( 3) link_BETA1-4 : angle 1.02596 ( 9) link_NAG-ASN : bond 0.00275 ( 12) link_NAG-ASN : angle 2.03262 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.638 Fit side-chains REVERT: C 335 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7702 (mmtm) REVERT: B 352 MET cc_start: 0.8132 (tpp) cc_final: 0.7783 (tpp) REVERT: D 86 ASP cc_start: 0.8011 (m-30) cc_final: 0.7737 (m-30) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.6460 time to fit residues: 180.0999 Evaluate side-chains 219 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 219 GLN A 314 ASN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118443 restraints weight = 54813.993| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.80 r_work: 0.2866 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16123 Z= 0.164 Angle : 0.620 6.801 21974 Z= 0.338 Chirality : 0.049 0.164 2625 Planarity : 0.004 0.034 2766 Dihedral : 5.242 38.484 2508 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.01 % Allowed : 5.23 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2043 helix: 2.25 (0.24), residues: 450 sheet: 0.84 (0.21), residues: 588 loop : -0.48 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 67 TYR 0.015 0.002 TYR A 438 PHE 0.014 0.002 PHE G 113 TRP 0.013 0.002 TRP H 116 HIS 0.006 0.002 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00302 (16089) covalent geometry : angle 0.61214 (21891) SS BOND : bond 0.00884 ( 19) SS BOND : angle 1.46178 ( 38) hydrogen bonds : bond 0.06424 ( 695) hydrogen bonds : angle 5.22458 ( 1830) link_BETA1-4 : bond 0.00809 ( 3) link_BETA1-4 : angle 0.44862 ( 9) link_NAG-ASN : bond 0.00491 ( 12) link_NAG-ASN : angle 2.04323 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.423 Fit side-chains REVERT: C 335 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8165 (mmtm) outliers start: 18 outliers final: 12 residues processed: 230 average time/residue: 0.6648 time to fit residues: 168.0297 Evaluate side-chains 230 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 86 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 51 ASN A 314 ASN E 39 GLN D 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122918 restraints weight = 44564.522| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.89 r_work: 0.2891 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16123 Z= 0.152 Angle : 0.594 6.842 21974 Z= 0.324 Chirality : 0.048 0.166 2625 Planarity : 0.004 0.035 2766 Dihedral : 4.980 27.864 2508 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.96 % Allowed : 5.79 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2043 helix: 2.29 (0.24), residues: 450 sheet: 0.90 (0.21), residues: 588 loop : -0.50 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 67 TYR 0.014 0.002 TYR B 438 PHE 0.012 0.002 PHE G 79 TRP 0.011 0.002 TRP H 116 HIS 0.005 0.002 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00278 (16089) covalent geometry : angle 0.58671 (21891) SS BOND : bond 0.00799 ( 19) SS BOND : angle 1.28839 ( 38) hydrogen bonds : bond 0.06135 ( 695) hydrogen bonds : angle 5.12587 ( 1830) link_BETA1-4 : bond 0.00689 ( 3) link_BETA1-4 : angle 0.58362 ( 9) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 2.09264 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.693 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 229 average time/residue: 0.6126 time to fit residues: 154.3607 Evaluate side-chains 231 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain D residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 134 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 139 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 314 ASN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115815 restraints weight = 46275.087| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.55 r_work: 0.2805 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16123 Z= 0.267 Angle : 0.790 7.650 21974 Z= 0.434 Chirality : 0.055 0.197 2625 Planarity : 0.005 0.033 2766 Dihedral : 5.537 30.690 2508 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.01 % Allowed : 5.96 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2043 helix: 1.92 (0.24), residues: 450 sheet: 0.64 (0.21), residues: 612 loop : -0.47 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 67 TYR 0.020 0.003 TYR B 438 PHE 0.020 0.003 PHE C 235 TRP 0.014 0.003 TRP H 116 HIS 0.007 0.003 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00526 (16089) covalent geometry : angle 0.77996 (21891) SS BOND : bond 0.01635 ( 19) SS BOND : angle 2.07741 ( 38) hydrogen bonds : bond 0.08325 ( 695) hydrogen bonds : angle 5.54066 ( 1830) link_BETA1-4 : bond 0.00806 ( 3) link_BETA1-4 : angle 0.49092 ( 9) link_NAG-ASN : bond 0.00778 ( 12) link_NAG-ASN : angle 2.45773 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.631 Fit side-chains REVERT: A 335 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8269 (mmtm) REVERT: C 335 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8245 (mmtm) REVERT: E 55 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8306 (mtm-85) outliers start: 18 outliers final: 10 residues processed: 229 average time/residue: 0.6511 time to fit residues: 163.7909 Evaluate side-chains 227 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain D residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 314 ASN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117512 restraints weight = 49760.155| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.45 r_work: 0.2826 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16123 Z= 0.207 Angle : 0.697 7.436 21974 Z= 0.383 Chirality : 0.052 0.181 2625 Planarity : 0.004 0.034 2766 Dihedral : 5.372 28.962 2508 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.01 % Allowed : 6.41 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2043 helix: 2.02 (0.24), residues: 450 sheet: 0.65 (0.21), residues: 612 loop : -0.49 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 67 TYR 0.016 0.002 TYR B 438 PHE 0.015 0.002 PHE C 235 TRP 0.013 0.002 TRP H 116 HIS 0.006 0.002 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00395 (16089) covalent geometry : angle 0.68784 (21891) SS BOND : bond 0.01201 ( 19) SS BOND : angle 1.74981 ( 38) hydrogen bonds : bond 0.07306 ( 695) hydrogen bonds : angle 5.38411 ( 1830) link_BETA1-4 : bond 0.00757 ( 3) link_BETA1-4 : angle 0.47899 ( 9) link_NAG-ASN : bond 0.00593 ( 12) link_NAG-ASN : angle 2.35934 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.655 Fit side-chains REVERT: C 335 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8243 (mmtm) REVERT: E 55 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8316 (mtm-85) outliers start: 18 outliers final: 13 residues processed: 233 average time/residue: 0.6812 time to fit residues: 175.1539 Evaluate side-chains 231 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 123 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 102 HIS A 314 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114747 restraints weight = 45235.865| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.49 r_work: 0.2786 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 16123 Z= 0.334 Angle : 0.895 8.017 21974 Z= 0.493 Chirality : 0.060 0.216 2625 Planarity : 0.006 0.058 2766 Dihedral : 5.792 29.443 2508 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.07 % Allowed : 6.35 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.18), residues: 2043 helix: 1.67 (0.24), residues: 450 sheet: 0.54 (0.21), residues: 612 loop : -0.47 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG G 67 TYR 0.025 0.003 TYR C 274 PHE 0.022 0.004 PHE C 235 TRP 0.016 0.004 TRP H 116 HIS 0.008 0.003 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00676 (16089) covalent geometry : angle 0.88473 (21891) SS BOND : bond 0.02050 ( 19) SS BOND : angle 2.31302 ( 38) hydrogen bonds : bond 0.09160 ( 695) hydrogen bonds : angle 5.70009 ( 1830) link_BETA1-4 : bond 0.00832 ( 3) link_BETA1-4 : angle 0.60064 ( 9) link_NAG-ASN : bond 0.01014 ( 12) link_NAG-ASN : angle 2.67384 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.766 Fit side-chains REVERT: C 335 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8163 (mppt) outliers start: 19 outliers final: 11 residues processed: 232 average time/residue: 0.6754 time to fit residues: 173.1120 Evaluate side-chains 232 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 9 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 102 HIS A 314 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120702 restraints weight = 54922.782| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.65 r_work: 0.2895 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16123 Z= 0.131 Angle : 0.575 7.065 21974 Z= 0.311 Chirality : 0.047 0.169 2625 Planarity : 0.004 0.036 2766 Dihedral : 4.998 22.601 2508 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.67 % Allowed : 7.08 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2043 helix: 2.27 (0.25), residues: 450 sheet: 0.73 (0.21), residues: 606 loop : -0.44 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.009 0.001 TYR B 438 PHE 0.016 0.001 PHE G 79 TRP 0.013 0.001 TRP I 33 HIS 0.006 0.002 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00240 (16089) covalent geometry : angle 0.56729 (21891) SS BOND : bond 0.00555 ( 19) SS BOND : angle 0.97365 ( 38) hydrogen bonds : bond 0.05400 ( 695) hydrogen bonds : angle 5.07400 ( 1830) link_BETA1-4 : bond 0.00732 ( 3) link_BETA1-4 : angle 0.56105 ( 9) link_NAG-ASN : bond 0.00330 ( 12) link_NAG-ASN : angle 2.23377 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.419 Fit side-chains REVERT: A 335 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8243 (mmtp) REVERT: C 335 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8198 (mmtm) outliers start: 12 outliers final: 9 residues processed: 231 average time/residue: 0.6069 time to fit residues: 154.2676 Evaluate side-chains 228 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain D residue 9 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 177 optimal weight: 0.0970 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 314 ASN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118448 restraints weight = 54931.737| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.67 r_work: 0.2858 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16123 Z= 0.159 Angle : 0.621 7.173 21974 Z= 0.337 Chirality : 0.049 0.172 2625 Planarity : 0.004 0.036 2766 Dihedral : 4.999 21.751 2508 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.67 % Allowed : 7.53 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2043 helix: 2.22 (0.24), residues: 450 sheet: 0.87 (0.21), residues: 585 loop : -0.48 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 67 TYR 0.013 0.002 TYR B 438 PHE 0.015 0.002 PHE I 79 TRP 0.012 0.002 TRP I 33 HIS 0.005 0.002 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00294 (16089) covalent geometry : angle 0.61361 (21891) SS BOND : bond 0.00842 ( 19) SS BOND : angle 1.38112 ( 38) hydrogen bonds : bond 0.06289 ( 695) hydrogen bonds : angle 5.17911 ( 1830) link_BETA1-4 : bond 0.00729 ( 3) link_BETA1-4 : angle 0.52556 ( 9) link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.17030 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.588 Fit side-chains REVERT: A 335 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8214 (mmtp) REVERT: C 335 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8139 (mppt) outliers start: 12 outliers final: 8 residues processed: 226 average time/residue: 0.5902 time to fit residues: 147.2113 Evaluate side-chains 223 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain D residue 9 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 107 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 14 optimal weight: 0.0570 chunk 40 optimal weight: 0.0670 chunk 185 optimal weight: 9.9990 chunk 144 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 314 ASN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124451 restraints weight = 50923.461| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.44 r_work: 0.2938 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16123 Z= 0.111 Angle : 0.530 7.204 21974 Z= 0.284 Chirality : 0.046 0.163 2625 Planarity : 0.004 0.037 2766 Dihedral : 4.563 20.561 2508 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.45 % Allowed : 7.98 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.18), residues: 2043 helix: 2.43 (0.25), residues: 447 sheet: 0.76 (0.21), residues: 606 loop : -0.50 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.009 0.001 TYR I 60 PHE 0.015 0.001 PHE I 79 TRP 0.012 0.001 TRP I 33 HIS 0.004 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00207 (16089) covalent geometry : angle 0.52325 (21891) SS BOND : bond 0.00337 ( 19) SS BOND : angle 0.79177 ( 38) hydrogen bonds : bond 0.04544 ( 695) hydrogen bonds : angle 4.82805 ( 1830) link_BETA1-4 : bond 0.00723 ( 3) link_BETA1-4 : angle 0.75635 ( 9) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 2.00790 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 229 time to evaluate : 0.677 Fit side-chains REVERT: C 335 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8158 (mppt) REVERT: B 251 GLU cc_start: 0.7356 (pm20) cc_final: 0.7003 (pm20) outliers start: 8 outliers final: 5 residues processed: 234 average time/residue: 0.6001 time to fit residues: 154.5300 Evaluate side-chains 224 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain D residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 42 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 14 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN H 78 GLN A 314 ASN A 459 GLN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122615 restraints weight = 51500.860| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.50 r_work: 0.2915 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16123 Z= 0.123 Angle : 0.559 7.237 21974 Z= 0.298 Chirality : 0.047 0.163 2625 Planarity : 0.004 0.037 2766 Dihedral : 4.538 19.992 2508 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.39 % Allowed : 8.26 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.18), residues: 2043 helix: 2.42 (0.25), residues: 450 sheet: 0.90 (0.21), residues: 594 loop : -0.48 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.010 0.001 TYR B 275 PHE 0.014 0.001 PHE I 79 TRP 0.013 0.001 TRP I 33 HIS 0.004 0.001 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00229 (16089) covalent geometry : angle 0.55170 (21891) SS BOND : bond 0.00518 ( 19) SS BOND : angle 1.19746 ( 38) hydrogen bonds : bond 0.05068 ( 695) hydrogen bonds : angle 4.86914 ( 1830) link_BETA1-4 : bond 0.00631 ( 3) link_BETA1-4 : angle 0.66018 ( 9) link_NAG-ASN : bond 0.00312 ( 12) link_NAG-ASN : angle 1.95016 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.657 Fit side-chains REVERT: A 335 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8246 (mppt) REVERT: C 335 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8160 (mppt) REVERT: B 251 GLU cc_start: 0.7357 (pm20) cc_final: 0.7005 (pm20) REVERT: D 55 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8285 (mtm110) outliers start: 7 outliers final: 5 residues processed: 229 average time/residue: 0.6520 time to fit residues: 164.2330 Evaluate side-chains 223 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain D residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 102 optimal weight: 0.0770 chunk 165 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 314 ASN C 395 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123130 restraints weight = 46949.275| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.36 r_work: 0.2911 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16123 Z= 0.124 Angle : 0.558 7.263 21974 Z= 0.298 Chirality : 0.047 0.164 2625 Planarity : 0.004 0.037 2766 Dihedral : 4.520 19.558 2508 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.39 % Allowed : 8.49 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.18), residues: 2043 helix: 2.40 (0.25), residues: 450 sheet: 0.90 (0.21), residues: 594 loop : -0.47 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.010 0.001 TYR B 438 PHE 0.014 0.001 PHE I 79 TRP 0.012 0.001 TRP I 33 HIS 0.004 0.001 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00231 (16089) covalent geometry : angle 0.55124 (21891) SS BOND : bond 0.00520 ( 19) SS BOND : angle 1.16271 ( 38) hydrogen bonds : bond 0.05092 ( 695) hydrogen bonds : angle 4.86448 ( 1830) link_BETA1-4 : bond 0.00624 ( 3) link_BETA1-4 : angle 0.69073 ( 9) link_NAG-ASN : bond 0.00299 ( 12) link_NAG-ASN : angle 1.93558 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8140.51 seconds wall clock time: 139 minutes 0.15 seconds (8340.15 seconds total)