Starting phenix.real_space_refine on Sat Jun 14 16:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua9_63982/06_2025/9ua9_63982.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua9_63982/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ua9_63982/06_2025/9ua9_63982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua9_63982/06_2025/9ua9_63982.map" model { file = "/net/cci-nas-00/data/ceres_data/9ua9_63982/06_2025/9ua9_63982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua9_63982/06_2025/9ua9_63982.cif" } resolution = 1.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.31, per 1000 atoms: 1.06 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: 3.54 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 2.37 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: 6.06 Time building geometry restraints manager: 4.26 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: 0.04 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 476 or resid 501 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 476 or resid 501 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 476 or resid 501 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 47.800 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.490 ------------------------------------------------------------------------------- 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 : 1.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (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 TRP 0.010 0.001 TRP I 33 HIS 0.005 0.001 HIS I 111 PHE 0.012 0.002 PHE G 113 TYR 0.012 0.001 TYR A 438 ARG 0.003 0.000 ARG I 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 12) link_NAG-ASN : angle 2.03262 ( 36) link_BETA1-4 : bond 0.00667 ( 3) link_BETA1-4 : angle 1.02596 ( 9) hydrogen bonds : bond 0.13055 ( 695) hydrogen bonds : angle 5.71519 ( 1830) SS BOND : bond 0.00617 ( 19) SS BOND : angle 1.16554 ( 38) covalent geometry : bond 0.00289 (16089) covalent geometry : angle 0.56696 (21891) *********************** 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 : 1.646 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: 1.3358 time to fit residues: 372.9371 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 : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121898 restraints weight = 52003.195| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.44 r_work: 0.2888 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16123 Z= 0.136 Angle : 0.566 6.330 21974 Z= 0.308 Chirality : 0.047 0.158 2625 Planarity : 0.004 0.035 2766 Dihedral : 5.108 39.385 2508 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.96 % Allowed : 5.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2043 helix: 2.37 (0.25), residues: 450 sheet: 0.81 (0.21), residues: 597 loop : -0.45 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 116 HIS 0.005 0.002 HIS I 111 PHE 0.012 0.002 PHE G 79 TYR 0.012 0.001 TYR A 438 ARG 0.003 0.000 ARG I 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 12) link_NAG-ASN : angle 1.98318 ( 36) link_BETA1-4 : bond 0.00734 ( 3) link_BETA1-4 : angle 0.50605 ( 9) hydrogen bonds : bond 0.05693 ( 695) hydrogen bonds : angle 5.11263 ( 1830) SS BOND : bond 0.00632 ( 19) SS BOND : angle 1.23708 ( 38) covalent geometry : bond 0.00248 (16089) covalent geometry : angle 0.55896 (21891) *********************** 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 242 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 2.161 Fit side-chains REVERT: C 335 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8165 (mmtm) REVERT: B 352 MET cc_start: 0.8579 (tpp) cc_final: 0.8305 (tpp) outliers start: 17 outliers final: 11 residues processed: 230 average time/residue: 1.4147 time to fit residues: 357.1153 Evaluate side-chains 227 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 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 91 THR Chi-restraints excluded: chain I residue 93 MET 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 3 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 A 459 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 = 0.3638 r_free = 0.3638 target = 0.145084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120471 restraints weight = 49290.948| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.37 r_work: 0.2877 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 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 = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16123 Z= 0.152 Angle : 0.593 6.743 21974 Z= 0.323 Chirality : 0.048 0.162 2625 Planarity : 0.004 0.034 2766 Dihedral : 4.946 28.046 2508 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.90 % Allowed : 5.90 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2043 helix: 2.31 (0.24), residues: 450 sheet: 0.80 (0.21), residues: 597 loop : -0.47 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 116 HIS 0.006 0.002 HIS I 111 PHE 0.013 0.002 PHE G 113 TYR 0.014 0.002 TYR B 438 ARG 0.004 0.001 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 12) link_NAG-ASN : angle 2.07031 ( 36) link_BETA1-4 : bond 0.00694 ( 3) link_BETA1-4 : angle 0.56454 ( 9) hydrogen bonds : bond 0.06163 ( 695) hydrogen bonds : angle 5.11439 ( 1830) SS BOND : bond 0.00810 ( 19) SS BOND : angle 1.30786 ( 38) covalent geometry : bond 0.00278 (16089) covalent geometry : angle 0.58551 (21891) *********************** 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 243 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 1.688 Fit side-chains REVERT: A 335 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8503 (tppp) outliers start: 16 outliers final: 10 residues processed: 232 average time/residue: 1.4269 time to fit residues: 363.2815 Evaluate side-chains 224 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 B residue 115 MET 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 132 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 172 optimal weight: 0.0170 chunk 7 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- 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 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 = 0.3599 r_free = 0.3599 target = 0.141872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116627 restraints weight = 49856.757| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.40 r_work: 0.2816 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16123 Z= 0.260 Angle : 0.774 7.644 21974 Z= 0.425 Chirality : 0.055 0.192 2625 Planarity : 0.005 0.033 2766 Dihedral : 5.496 30.562 2508 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.01 % Allowed : 5.62 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2043 helix: 1.97 (0.24), residues: 450 sheet: 0.66 (0.21), residues: 612 loop : -0.47 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 116 HIS 0.007 0.003 HIS I 111 PHE 0.019 0.003 PHE C 235 TYR 0.020 0.003 TYR B 438 ARG 0.008 0.001 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 12) link_NAG-ASN : angle 2.44457 ( 36) link_BETA1-4 : bond 0.00796 ( 3) link_BETA1-4 : angle 0.48390 ( 9) hydrogen bonds : bond 0.08174 ( 695) hydrogen bonds : angle 5.50168 ( 1830) SS BOND : bond 0.01595 ( 19) SS BOND : angle 2.03864 ( 38) covalent geometry : bond 0.00513 (16089) covalent geometry : angle 0.76405 (21891) *********************** 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 238 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 1.653 Fit side-chains REVERT: C 335 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8253 (mmtm) REVERT: E 55 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8311 (mtm-85) outliers start: 18 outliers final: 11 residues processed: 226 average time/residue: 1.3668 time to fit residues: 340.1366 Evaluate side-chains 227 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 B residue 115 MET Chi-restraints excluded: chain B residue 335 LYS 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 173 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 182 optimal weight: 0.0060 chunk 67 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 102 HIS A 314 ASN E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117402 restraints weight = 51277.948| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.52 r_work: 0.2827 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16123 Z= 0.200 Angle : 0.685 7.378 21974 Z= 0.376 Chirality : 0.051 0.179 2625 Planarity : 0.004 0.034 2766 Dihedral : 5.325 28.488 2508 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.96 % Allowed : 6.24 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2043 helix: 2.06 (0.24), residues: 450 sheet: 0.66 (0.21), residues: 612 loop : -0.48 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 116 HIS 0.006 0.002 HIS I 111 PHE 0.014 0.002 PHE C 235 TYR 0.016 0.002 TYR B 438 ARG 0.006 0.001 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 2.33878 ( 36) link_BETA1-4 : bond 0.00749 ( 3) link_BETA1-4 : angle 0.48510 ( 9) hydrogen bonds : bond 0.07182 ( 695) hydrogen bonds : angle 5.35737 ( 1830) SS BOND : bond 0.01158 ( 19) SS BOND : angle 1.70832 ( 38) covalent geometry : bond 0.00380 (16089) covalent geometry : angle 0.67588 (21891) *********************** 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 242 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 1.673 Fit side-chains REVERT: A 335 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8281 (mmtm) REVERT: C 335 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8239 (mmtm) outliers start: 17 outliers final: 13 residues processed: 232 average time/residue: 1.3624 time to fit residues: 348.8658 Evaluate side-chains 229 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 B residue 115 MET 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 144 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 129 optimal weight: 0.0170 chunk 6 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- 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 E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118808 restraints weight = 52346.238| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.42 r_work: 0.2844 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16123 Z= 0.176 Angle : 0.644 7.165 21974 Z= 0.352 Chirality : 0.050 0.173 2625 Planarity : 0.004 0.035 2766 Dihedral : 5.163 24.341 2508 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.96 % Allowed : 6.69 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2043 helix: 2.15 (0.24), residues: 450 sheet: 0.85 (0.21), residues: 585 loop : -0.47 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 116 HIS 0.006 0.002 HIS I 111 PHE 0.013 0.002 PHE G 79 TYR 0.015 0.002 TYR B 438 ARG 0.005 0.001 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 12) link_NAG-ASN : angle 2.26719 ( 36) link_BETA1-4 : bond 0.00728 ( 3) link_BETA1-4 : angle 0.51692 ( 9) hydrogen bonds : bond 0.06688 ( 695) hydrogen bonds : angle 5.26115 ( 1830) SS BOND : bond 0.00980 ( 19) SS BOND : angle 1.51550 ( 38) covalent geometry : bond 0.00329 (16089) covalent geometry : angle 0.63571 (21891) *********************** 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 237 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 1.672 Fit side-chains REVERT: C 335 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8210 (mmtm) REVERT: B 251 GLU cc_start: 0.7479 (pm20) cc_final: 0.7141 (pm20) outliers start: 17 outliers final: 14 residues processed: 227 average time/residue: 1.3497 time to fit residues: 337.5778 Evaluate side-chains 231 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 C residue 399 ARG Chi-restraints excluded: chain B residue 115 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 194 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118334 restraints weight = 53162.464| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.45 r_work: 0.2838 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16123 Z= 0.189 Angle : 0.669 7.309 21974 Z= 0.366 Chirality : 0.051 0.179 2625 Planarity : 0.004 0.034 2766 Dihedral : 5.196 22.479 2508 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.90 % Allowed : 6.97 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2043 helix: 2.08 (0.24), residues: 450 sheet: 0.82 (0.21), residues: 591 loop : -0.52 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 116 HIS 0.007 0.002 HIS I 111 PHE 0.013 0.002 PHE C 235 TYR 0.016 0.002 TYR B 438 ARG 0.005 0.001 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 12) link_NAG-ASN : angle 2.28678 ( 36) link_BETA1-4 : bond 0.00732 ( 3) link_BETA1-4 : angle 0.52369 ( 9) hydrogen bonds : bond 0.06996 ( 695) hydrogen bonds : angle 5.31065 ( 1830) SS BOND : bond 0.01086 ( 19) SS BOND : angle 1.61734 ( 38) covalent geometry : bond 0.00355 (16089) covalent geometry : angle 0.66033 (21891) *********************** 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 235 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 1.932 Fit side-chains REVERT: A 335 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8263 (mmtm) REVERT: C 335 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8207 (mmtm) outliers start: 16 outliers final: 14 residues processed: 224 average time/residue: 1.5373 time to fit residues: 379.0039 Evaluate side-chains 232 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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 B residue 115 MET Chi-restraints excluded: chain B residue 335 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 175 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 123 optimal weight: 0.0670 chunk 23 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121473 restraints weight = 53501.618| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.63 r_work: 0.2904 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16123 Z= 0.124 Angle : 0.552 7.257 21974 Z= 0.298 Chirality : 0.047 0.164 2625 Planarity : 0.004 0.035 2766 Dihedral : 4.748 21.356 2508 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 7.36 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2043 helix: 2.38 (0.25), residues: 450 sheet: 0.84 (0.21), residues: 594 loop : -0.44 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 33 HIS 0.004 0.001 HIS A 102 PHE 0.013 0.001 PHE G 79 TYR 0.009 0.001 TYR I 60 ARG 0.004 0.000 ARG F 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 2.10139 ( 36) link_BETA1-4 : bond 0.00691 ( 3) link_BETA1-4 : angle 0.66070 ( 9) hydrogen bonds : bond 0.05140 ( 695) hydrogen bonds : angle 4.95028 ( 1830) SS BOND : bond 0.00501 ( 19) SS BOND : angle 0.97341 ( 38) covalent geometry : bond 0.00228 (16089) covalent geometry : angle 0.54439 (21891) *********************** 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 238 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 2.170 Fit side-chains REVERT: A 335 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8254 (mmtm) REVERT: C 335 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8147 (mppt) REVERT: B 251 GLU cc_start: 0.7437 (pm20) cc_final: 0.7091 (pm20) outliers start: 10 outliers final: 8 residues processed: 232 average time/residue: 1.5201 time to fit residues: 390.4784 Evaluate side-chains 228 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G 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 Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 128 optimal weight: 0.0570 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119170 restraints weight = 56096.460| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.64 r_work: 0.2868 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16123 Z= 0.155 Angle : 0.608 7.258 21974 Z= 0.330 Chirality : 0.048 0.170 2625 Planarity : 0.004 0.035 2766 Dihedral : 4.840 21.304 2508 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.56 % Allowed : 7.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2043 helix: 2.27 (0.24), residues: 450 sheet: 0.92 (0.21), residues: 585 loop : -0.48 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 33 HIS 0.005 0.002 HIS I 111 PHE 0.012 0.002 PHE G 79 TYR 0.013 0.002 TYR A 438 ARG 0.004 0.000 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 12) link_NAG-ASN : angle 2.10814 ( 36) link_BETA1-4 : bond 0.00684 ( 3) link_BETA1-4 : angle 0.60248 ( 9) hydrogen bonds : bond 0.06126 ( 695) hydrogen bonds : angle 5.09882 ( 1830) SS BOND : bond 0.00814 ( 19) SS BOND : angle 1.52270 ( 38) covalent geometry : bond 0.00287 (16089) covalent geometry : angle 0.59997 (21891) *********************** 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 230 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 1.799 Fit side-chains REVERT: A 335 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8250 (mmtm) REVERT: C 335 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8137 (mppt) REVERT: C 395 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 251 GLU cc_start: 0.7418 (pm20) cc_final: 0.7087 (pm20) outliers start: 10 outliers final: 9 residues processed: 225 average time/residue: 1.3972 time to fit residues: 345.3916 Evaluate side-chains 225 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 123 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 Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 104 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119513 restraints weight = 49974.948| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.55 r_work: 0.2873 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 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 0.037 16123 Z= 0.151 Angle : 0.604 7.298 21974 Z= 0.328 Chirality : 0.048 0.169 2625 Planarity : 0.004 0.035 2766 Dihedral : 4.832 21.310 2508 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 7.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2043 helix: 2.26 (0.24), residues: 450 sheet: 0.93 (0.21), residues: 585 loop : -0.49 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 33 HIS 0.005 0.002 HIS I 111 PHE 0.012 0.002 PHE G 79 TYR 0.013 0.002 TYR A 438 ARG 0.004 0.000 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 2.10544 ( 36) link_BETA1-4 : bond 0.00677 ( 3) link_BETA1-4 : angle 0.62321 ( 9) hydrogen bonds : bond 0.06043 ( 695) hydrogen bonds : angle 5.09637 ( 1830) SS BOND : bond 0.00774 ( 19) SS BOND : angle 1.43609 ( 38) covalent geometry : bond 0.00281 (16089) covalent geometry : angle 0.59584 (21891) ********************** 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 229 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 1.712 Fit side-chains REVERT: A 335 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8215 (mmtp) REVERT: C 335 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8140 (mppt) outliers start: 10 outliers final: 9 residues processed: 224 average time/residue: 1.7346 time to fit residues: 428.3794 Evaluate side-chains 226 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 123 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 D residue 9 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 182 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3631 r_free = 0.3631 target = 0.144428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119321 restraints weight = 51267.085| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.49 r_work: 0.2859 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- 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 = 0.24 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16123 Z= 0.162 Angle : 0.624 7.285 21974 Z= 0.339 Chirality : 0.049 0.175 2625 Planarity : 0.004 0.034 2766 Dihedral : 4.894 21.386 2508 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.73 % Allowed : 7.59 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2043 helix: 2.25 (0.24), residues: 450 sheet: 0.92 (0.21), residues: 585 loop : -0.49 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 116 HIS 0.005 0.002 HIS I 111 PHE 0.012 0.002 PHE G 79 TYR 0.014 0.002 TYR A 438 ARG 0.004 0.001 ARG G 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 12) link_NAG-ASN : angle 2.13568 ( 36) link_BETA1-4 : bond 0.00687 ( 3) link_BETA1-4 : angle 0.61396 ( 9) hydrogen bonds : bond 0.06343 ( 695) hydrogen bonds : angle 5.15325 ( 1830) SS BOND : bond 0.00868 ( 19) SS BOND : angle 1.54216 ( 38) covalent geometry : bond 0.00301 (16089) covalent geometry : angle 0.61569 (21891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17768.01 seconds wall clock time: 306 minutes 22.50 seconds (18382.50 seconds total)