Starting phenix.real_space_refine on Sat May 17 18:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uaa_63983/05_2025/9uaa_63983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uaa_63983/05_2025/9uaa_63983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uaa_63983/05_2025/9uaa_63983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uaa_63983/05_2025/9uaa_63983.map" model { file = "/net/cci-nas-00/data/ceres_data/9uaa_63983/05_2025/9uaa_63983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uaa_63983/05_2025/9uaa_63983.cif" } resolution = 2.22 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= 0.082 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 72 5.16 5 C 9927 2.51 5 N 2550 2.21 5 O 3445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15994 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3375 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 bond proxies already assigned to first conformer: 3405 Chain: "F" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 996 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 996 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "I" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 996 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "B" Number of atoms: 3375 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 bond proxies already assigned to first conformer: 3405 Chain: "C" Number of atoms: 3375 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 bond proxies already assigned to first conformer: 3405 Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} 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: "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: "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: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASN A 155 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 155 " 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 C 155 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 155 " occ=0.50 Time building chain proxies: 14.24, per 1000 atoms: 0.89 Number of scatterers: 15994 At special positions: 0 Unit cell: (141.1, 148.57, 107.9, 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 72 16.00 O 3445 8.00 N 2550 7.00 C 9927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 87 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 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 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=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 87 " distance=2.05 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.05 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 NAG-ASN " NAG A 501 " - " ASN A 99 " " NAG A 502 " - " ASN A 414 " " NAG A 503 " - " ASN A 67 " " NAG B 501 " - " ASN B 99 " " NAG B 502 " - " ASN B 414 " " NAG B 503 " - " ASN B 67 " " NAG C 501 " - " ASN C 99 " " NAG C 502 " - " ASN C 414 " " NAG C 503 " - " ASN C 67 " Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 2.9 seconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 30 sheets defined 28.5% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.768A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.536A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.596A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.664A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.276A 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: 4.620A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.557A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) 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: 4.726A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.697A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (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: 3.642A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.623A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 removed outlier: 4.167A pdb=" N THR G 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 66 removed outlier: 3.753A pdb=" N LYS H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 66' Processing helix chain 'H' and resid 88 through 92 removed outlier: 4.156A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.702A pdb=" N LYS I 66 " --> pdb=" O PRO I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'I' and resid 88 through 92 removed outlier: 4.148A pdb=" N THR I 92 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.767A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.606A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.676A pdb=" N ASN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 3.669A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.380A 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: 4.617A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.500A pdb=" N SER B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) 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: 4.831A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.988A 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: 3.678A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (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: 3.636A pdb=" N GLU B 441 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.623A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.798A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.588A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.683A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 3.693A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.309A 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: 4.686A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.555A pdb=" N SER C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) 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: 4.809A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.916A 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: 3.755A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (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: 3.603A pdb=" N GLU C 441 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 471 removed outlier: 3.632A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 11.251A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 270 removed outlier: 3.615A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 removed outlier: 7.002A pdb=" N ILE A 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.750A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR F 86 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 84 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR F 96 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 61 removed outlier: 6.662A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR G 51 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP G 35 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG G 34 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ARG G 99 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP G 117 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 61 removed outlier: 6.662A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR G 51 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP G 35 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG G 34 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 93 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL G 123 " --> pdb=" O TYR G 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.656A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG H 34 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG H 99 " --> pdb=" O ASP H 117 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP H 117 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.656A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG H 34 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA H 93 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 123 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'I' and resid 59 through 61 removed outlier: 6.655A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 34 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG I 99 " --> pdb=" O ASP I 117 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP I 117 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 59 through 61 removed outlier: 6.655A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 34 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 93 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL I 123 " --> pdb=" O TYR I 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 158 through 161 removed outlier: 5.129A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.406A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY B 264 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR B 281 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE B 266 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG B 279 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 268 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AC5, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC6, first strand: chain 'C' and resid 158 through 162 removed outlier: 11.298A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 263 through 270 removed outlier: 5.848A pdb=" N GLY C 264 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR C 281 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE C 266 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG C 279 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 268 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 276 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL C 58 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 278 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 56 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 280 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR C 54 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE C 282 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.779A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 86 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 84 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 96 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.784A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 86 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 84 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 96 " --> pdb=" O GLN D 89 " (cutoff:3.500A) 697 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: 5.45 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5007 1.35 - 1.47: 3725 1.47 - 1.59: 7105 1.59 - 1.72: 0 1.72 - 1.84: 102 Bond restraints: 15939 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.40e+00 ... (remaining 15934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 20757 1.39 - 2.78: 773 2.78 - 4.17: 123 4.17 - 5.56: 34 5.56 - 6.95: 6 Bond angle restraints: 21693 Sorted by residual: angle pdb=" N GLY E 100 " pdb=" CA GLY E 100 " pdb=" C GLY E 100 " ideal model delta sigma weight residual 112.48 116.84 -4.36 1.21e+00 6.83e-01 1.30e+01 angle pdb=" N GLY D 100 " pdb=" CA GLY D 100 " pdb=" C GLY D 100 " ideal model delta sigma weight residual 112.48 116.80 -4.32 1.21e+00 6.83e-01 1.27e+01 angle pdb=" N GLY F 100 " pdb=" CA GLY F 100 " pdb=" C GLY F 100 " ideal model delta sigma weight residual 112.48 116.75 -4.27 1.21e+00 6.83e-01 1.25e+01 angle pdb=" N MET C 138 " pdb=" CA MET C 138 " pdb=" C MET C 138 " ideal model delta sigma weight residual 111.71 115.05 -3.34 1.15e+00 7.56e-01 8.44e+00 angle pdb=" N MET A 138 " pdb=" CA MET A 138 " pdb=" C MET A 138 " ideal model delta sigma weight residual 111.71 114.86 -3.15 1.15e+00 7.56e-01 7.49e+00 ... (remaining 21688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8982 17.86 - 35.71: 616 35.71 - 53.57: 101 53.57 - 71.43: 38 71.43 - 89.29: 13 Dihedral angle restraints: 9750 sinusoidal: 3885 harmonic: 5865 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 97 " pdb=" CB CYS I 97 " ideal model delta sinusoidal sigma weight residual 93.00 50.86 42.14 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " pdb=" CB CYS G 97 " ideal model delta sinusoidal sigma weight residual 93.00 53.29 39.71 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CA ILE B 288 " pdb=" C ILE B 288 " pdb=" N GLN B 289 " pdb=" CA GLN B 289 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 9747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1636 0.038 - 0.077: 651 0.077 - 0.115: 240 0.115 - 0.154: 68 0.154 - 0.192: 3 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 2595 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 119 " -0.010 2.00e-02 2.50e+03 9.80e-03 2.40e+00 pdb=" CG TRP H 119 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP H 119 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP H 119 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 119 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 119 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 119 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 119 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 119 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 220 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO C 221 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 220 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 221 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " -0.020 5.00e-02 4.00e+02 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 176 2.67 - 3.23: 14477 3.23 - 3.78: 23985 3.78 - 4.34: 35070 4.34 - 4.90: 54496 Nonbonded interactions: 128204 Sorted by model distance: nonbonded pdb=" O GLY E 30 " pdb=" OH TYR E 71 " model vdw 2.110 3.040 nonbonded pdb=" O GLY F 30 " pdb=" OH TYR F 71 " model vdw 2.115 3.040 nonbonded pdb=" O GLY D 30 " pdb=" OH TYR D 71 " model vdw 2.126 3.040 nonbonded pdb=" NH1 ARG F 61 " pdb=" O SER F 77 " model vdw 2.201 3.120 nonbonded pdb=" OE2 GLU A 152 " pdb=" OG SER A 273 " model vdw 2.218 3.040 ... (remaining 128199 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 154 or resid 156 through 471 or resid 501 throu \ gh 503)) selection = (chain 'B' and (resid 27 through 154 or resid 156 through 471 or resid 501 throu \ gh 503)) selection = (chain 'C' and (resid 27 through 154 or resid 156 through 471 or resid 501 throu \ gh 503)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.440 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.340 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.030 15963 Z= 0.176 Angle : 0.660 6.949 21750 Z= 0.361 Chirality : 0.049 0.192 2598 Planarity : 0.004 0.037 2736 Dihedral : 13.037 89.287 5943 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.08 (0.18), residues: 1998 helix: 1.56 (0.25), residues: 426 sheet: 0.62 (0.21), residues: 585 loop : -0.99 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 119 HIS 0.006 0.001 HIS B 102 PHE 0.014 0.002 PHE C 376 TYR 0.017 0.002 TYR B 135 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 2.67911 ( 27) hydrogen bonds : bond 0.15861 ( 661) hydrogen bonds : angle 7.09458 ( 1830) SS BOND : bond 0.00940 ( 15) SS BOND : angle 1.92051 ( 30) covalent geometry : bond 0.00325 (15939) covalent geometry : angle 0.64983 (21693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.759 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.5102 time to fit residues: 265.6204 Evaluate side-chains 148 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.0060 chunk 82 optimal weight: 0.0570 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS B 350 ASN C 162 GLN C 350 ASN D 27 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.188287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149009 restraints weight = 33450.167| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 5.12 r_work: 0.3250 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15963 Z= 0.118 Angle : 0.533 5.967 21750 Z= 0.292 Chirality : 0.045 0.149 2598 Planarity : 0.004 0.034 2736 Dihedral : 5.669 59.571 2346 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.51 % Allowed : 3.87 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.32 (0.19), residues: 1998 helix: 2.14 (0.26), residues: 408 sheet: 0.70 (0.20), residues: 612 loop : -0.97 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 48 HIS 0.006 0.001 HIS B 102 PHE 0.010 0.001 PHE I 80 TYR 0.015 0.001 TYR B 135 ARG 0.003 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 9) link_NAG-ASN : angle 2.12965 ( 27) hydrogen bonds : bond 0.04847 ( 661) hydrogen bonds : angle 5.67366 ( 1830) SS BOND : bond 0.00674 ( 15) SS BOND : angle 1.53096 ( 30) covalent geometry : bond 0.00207 (15939) covalent geometry : angle 0.52529 (21693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 1.730 Fit side-chains REVERT: F 50 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7467 (mtm110) REVERT: B 406 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7202 (pm20) outliers start: 9 outliers final: 3 residues processed: 162 average time/residue: 1.4586 time to fit residues: 258.8557 Evaluate side-chains 155 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 162 optimal weight: 0.0980 chunk 128 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN B 102 HIS B 350 ASN C 162 GLN C 350 ASN E 27 GLN D 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145620 restraints weight = 30799.972| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.88 r_work: 0.3205 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15963 Z= 0.155 Angle : 0.608 6.211 21750 Z= 0.332 Chirality : 0.048 0.175 2598 Planarity : 0.004 0.036 2736 Dihedral : 5.660 56.266 2346 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.79 % Allowed : 6.17 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.23 (0.18), residues: 1998 helix: 2.11 (0.26), residues: 408 sheet: 0.65 (0.21), residues: 582 loop : -1.00 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.005 0.001 HIS A 102 PHE 0.013 0.002 PHE C 376 TYR 0.016 0.002 TYR G 51 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 9) link_NAG-ASN : angle 2.44622 ( 27) hydrogen bonds : bond 0.06165 ( 661) hydrogen bonds : angle 5.75010 ( 1830) SS BOND : bond 0.00834 ( 15) SS BOND : angle 1.73173 ( 30) covalent geometry : bond 0.00283 (15939) covalent geometry : angle 0.59950 (21693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.606 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 160 average time/residue: 1.5312 time to fit residues: 267.5387 Evaluate side-chains 160 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN F 34 HIS B 102 HIS B 350 ASN C 162 GLN C 350 ASN E 27 GLN E 34 HIS D 27 GLN D 34 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142830 restraints weight = 32742.265| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 5.07 r_work: 0.3157 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15963 Z= 0.219 Angle : 0.732 7.355 21750 Z= 0.400 Chirality : 0.052 0.207 2598 Planarity : 0.005 0.037 2736 Dihedral : 5.944 46.950 2346 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.95 % Allowed : 7.97 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.03 (0.18), residues: 1998 helix: 1.87 (0.26), residues: 408 sheet: 0.51 (0.21), residues: 582 loop : -1.08 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 119 HIS 0.006 0.001 HIS A 102 PHE 0.015 0.002 PHE H 80 TYR 0.023 0.002 TYR I 51 ARG 0.005 0.001 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 9) link_NAG-ASN : angle 3.09462 ( 27) hydrogen bonds : bond 0.07612 ( 661) hydrogen bonds : angle 6.09486 ( 1830) SS BOND : bond 0.01152 ( 15) SS BOND : angle 2.19624 ( 30) covalent geometry : bond 0.00427 (15939) covalent geometry : angle 0.72065 (21693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.615 Fit side-chains REVERT: A 139 LYS cc_start: 0.8258 (tppt) cc_final: 0.8034 (mmtt) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 1.5991 time to fit residues: 274.8688 Evaluate side-chains 154 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 162 GLN E 27 GLN E 34 HIS E 88 GLN D 27 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141398 restraints weight = 41267.201| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 5.10 r_work: 0.3197 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15963 Z= 0.140 Angle : 0.580 5.938 21750 Z= 0.316 Chirality : 0.047 0.174 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.314 40.226 2346 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.01 % Allowed : 8.75 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.17 (0.18), residues: 1998 helix: 2.11 (0.26), residues: 408 sheet: 0.57 (0.21), residues: 582 loop : -1.04 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 48 HIS 0.006 0.001 HIS A 102 PHE 0.011 0.001 PHE C 376 TYR 0.012 0.001 TYR H 51 ARG 0.003 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 9) link_NAG-ASN : angle 2.55524 ( 27) hydrogen bonds : bond 0.05631 ( 661) hydrogen bonds : angle 5.68153 ( 1830) SS BOND : bond 0.00782 ( 15) SS BOND : angle 1.58399 ( 30) covalent geometry : bond 0.00252 (15939) covalent geometry : angle 0.57040 (21693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.608 Fit side-chains REVERT: A 164 THR cc_start: 0.6575 (OUTLIER) cc_final: 0.6172 (p) REVERT: B 406 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: C 164 THR cc_start: 0.6499 (OUTLIER) cc_final: 0.6165 (p) outliers start: 18 outliers final: 7 residues processed: 160 average time/residue: 1.5868 time to fit residues: 277.3315 Evaluate side-chains 157 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 182 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS F 88 GLN B 102 HIS C 102 HIS C 162 GLN E 27 GLN E 88 GLN D 27 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144969 restraints weight = 33711.690| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 4.99 r_work: 0.3169 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15963 Z= 0.164 Angle : 0.625 6.402 21750 Z= 0.341 Chirality : 0.048 0.188 2598 Planarity : 0.004 0.034 2736 Dihedral : 5.313 40.321 2346 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.07 % Allowed : 9.09 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.10 (0.18), residues: 1998 helix: 2.05 (0.26), residues: 408 sheet: 0.53 (0.21), residues: 582 loop : -1.08 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 48 HIS 0.007 0.001 HIS A 102 PHE 0.013 0.002 PHE C 376 TYR 0.017 0.002 TYR H 51 ARG 0.003 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 9) link_NAG-ASN : angle 2.67114 ( 27) hydrogen bonds : bond 0.06377 ( 661) hydrogen bonds : angle 5.75935 ( 1830) SS BOND : bond 0.00865 ( 15) SS BOND : angle 1.71439 ( 30) covalent geometry : bond 0.00305 (15939) covalent geometry : angle 0.61567 (21693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.674 Fit side-chains REVERT: A 164 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6187 (p) REVERT: B 164 THR cc_start: 0.6229 (OUTLIER) cc_final: 0.5934 (t) REVERT: B 406 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: C 164 THR cc_start: 0.6529 (OUTLIER) cc_final: 0.6165 (p) outliers start: 19 outliers final: 9 residues processed: 159 average time/residue: 1.5452 time to fit residues: 267.5024 Evaluate side-chains 160 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 136 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN B 102 HIS C 102 HIS C 162 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142611 restraints weight = 39273.867| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 6.02 r_work: 0.3167 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15963 Z= 0.200 Angle : 0.692 6.926 21750 Z= 0.378 Chirality : 0.051 0.205 2598 Planarity : 0.004 0.036 2736 Dihedral : 5.531 42.843 2346 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.23 % Allowed : 9.15 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.02 (0.18), residues: 1998 helix: 1.93 (0.26), residues: 408 sheet: 0.48 (0.20), residues: 582 loop : -1.10 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 35 HIS 0.008 0.002 HIS A 102 PHE 0.015 0.002 PHE C 376 TYR 0.019 0.002 TYR I 51 ARG 0.004 0.001 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 9) link_NAG-ASN : angle 2.92122 ( 27) hydrogen bonds : bond 0.07136 ( 661) hydrogen bonds : angle 5.93344 ( 1830) SS BOND : bond 0.01002 ( 15) SS BOND : angle 1.88749 ( 30) covalent geometry : bond 0.00386 (15939) covalent geometry : angle 0.68158 (21693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.716 Fit side-chains REVERT: A 164 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6259 (p) REVERT: F 46 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6068 (tp) REVERT: B 164 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.5991 (t) REVERT: C 164 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.6231 (p) REVERT: D 88 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6430 (pp30) outliers start: 22 outliers final: 10 residues processed: 159 average time/residue: 1.6419 time to fit residues: 284.1832 Evaluate side-chains 156 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN B 102 HIS C 102 HIS C 162 GLN E 27 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145996 restraints weight = 32969.805| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 4.96 r_work: 0.3185 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15963 Z= 0.145 Angle : 0.587 6.026 21750 Z= 0.321 Chirality : 0.047 0.181 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.201 40.628 2346 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.01 % Allowed : 9.32 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.12 (0.18), residues: 1998 helix: 2.11 (0.26), residues: 408 sheet: 0.51 (0.20), residues: 582 loop : -1.06 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 48 HIS 0.007 0.002 HIS A 102 PHE 0.011 0.001 PHE C 376 TYR 0.013 0.001 TYR H 51 ARG 0.002 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 9) link_NAG-ASN : angle 2.62078 ( 27) hydrogen bonds : bond 0.05791 ( 661) hydrogen bonds : angle 5.67113 ( 1830) SS BOND : bond 0.00798 ( 15) SS BOND : angle 1.56677 ( 30) covalent geometry : bond 0.00263 (15939) covalent geometry : angle 0.57756 (21693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.755 Fit side-chains REVERT: A 164 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6202 (p) REVERT: B 164 THR cc_start: 0.6262 (OUTLIER) cc_final: 0.5960 (t) REVERT: C 164 THR cc_start: 0.6553 (OUTLIER) cc_final: 0.6160 (p) outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 1.6213 time to fit residues: 279.1511 Evaluate side-chains 156 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 176 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 102 HIS C 162 GLN E 34 HIS D 27 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.182700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126454 restraints weight = 46617.596| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.96 r_work: 0.3181 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15963 Z= 0.187 Angle : 0.670 6.885 21750 Z= 0.365 Chirality : 0.050 0.201 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.417 42.090 2346 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.84 % Allowed : 9.60 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.03 (0.18), residues: 1998 helix: 1.97 (0.26), residues: 408 sheet: 0.46 (0.20), residues: 582 loop : -1.10 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 35 HIS 0.008 0.002 HIS C 102 PHE 0.015 0.002 PHE C 376 TYR 0.018 0.002 TYR I 51 ARG 0.004 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 2.83662 ( 27) hydrogen bonds : bond 0.06872 ( 661) hydrogen bonds : angle 5.86185 ( 1830) SS BOND : bond 0.00953 ( 15) SS BOND : angle 1.83266 ( 30) covalent geometry : bond 0.00356 (15939) covalent geometry : angle 0.65936 (21693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.646 Fit side-chains REVERT: A 164 THR cc_start: 0.6679 (OUTLIER) cc_final: 0.6267 (p) REVERT: B 164 THR cc_start: 0.6416 (OUTLIER) cc_final: 0.6109 (t) REVERT: C 164 THR cc_start: 0.6616 (OUTLIER) cc_final: 0.6295 (p) REVERT: D 88 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6541 (pp30) outliers start: 15 outliers final: 8 residues processed: 151 average time/residue: 1.5959 time to fit residues: 263.1327 Evaluate side-chains 151 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 135 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS F 27 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 102 HIS C 162 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141331 restraints weight = 42545.611| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 5.17 r_work: 0.3186 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15963 Z= 0.146 Angle : 0.589 6.208 21750 Z= 0.321 Chirality : 0.047 0.182 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.151 39.966 2346 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.62 % Allowed : 9.88 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.13 (0.18), residues: 1998 helix: 2.13 (0.26), residues: 408 sheet: 0.51 (0.20), residues: 582 loop : -1.07 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 48 HIS 0.008 0.002 HIS C 102 PHE 0.012 0.002 PHE C 376 TYR 0.013 0.001 TYR I 51 ARG 0.002 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 9) link_NAG-ASN : angle 2.58574 ( 27) hydrogen bonds : bond 0.05797 ( 661) hydrogen bonds : angle 5.65265 ( 1830) SS BOND : bond 0.00794 ( 15) SS BOND : angle 1.63758 ( 30) covalent geometry : bond 0.00264 (15939) covalent geometry : angle 0.57971 (21693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.626 Fit side-chains REVERT: A 164 THR cc_start: 0.6599 (OUTLIER) cc_final: 0.6203 (p) REVERT: B 164 THR cc_start: 0.6332 (OUTLIER) cc_final: 0.6035 (t) REVERT: C 164 THR cc_start: 0.6568 (OUTLIER) cc_final: 0.6175 (p) REVERT: D 88 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6346 (pp30) outliers start: 11 outliers final: 7 residues processed: 153 average time/residue: 1.5386 time to fit residues: 256.9488 Evaluate side-chains 153 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 88 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 184 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 41 optimal weight: 0.0040 chunk 112 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN B 102 HIS C 102 HIS C 162 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147583 restraints weight = 36734.721| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 5.86 r_work: 0.3253 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15963 Z= 0.106 Angle : 0.508 5.865 21750 Z= 0.275 Chirality : 0.045 0.164 2598 Planarity : 0.004 0.034 2736 Dihedral : 4.606 33.012 2346 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.79 % Allowed : 9.88 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.32 (0.18), residues: 1998 helix: 2.41 (0.26), residues: 408 sheet: 0.61 (0.20), residues: 612 loop : -1.04 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 48 HIS 0.008 0.001 HIS B 102 PHE 0.009 0.001 PHE C 253 TYR 0.013 0.001 TYR C 275 ARG 0.001 0.000 ARG I 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 9) link_NAG-ASN : angle 2.08473 ( 27) hydrogen bonds : bond 0.04244 ( 661) hydrogen bonds : angle 5.24529 ( 1830) SS BOND : bond 0.00588 ( 15) SS BOND : angle 1.31062 ( 30) covalent geometry : bond 0.00191 (15939) covalent geometry : angle 0.50081 (21693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15475.45 seconds wall clock time: 273 minutes 50.20 seconds (16430.20 seconds total)