Starting phenix.real_space_refine on Thu Sep 18 10:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uaa_63983/09_2025/9uaa_63983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uaa_63983/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9uaa_63983/09_2025/9uaa_63983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uaa_63983/09_2025/9uaa_63983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uaa_63983/09_2025/9uaa_63983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uaa_63983/09_2025/9uaa_63983.map" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.082 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.38, per 1000 atoms: 0.34 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: 1.22 Conformation dependent library (CDL) restraints added in 944.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.58 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: 3.08 Time building geometry restraints manager: 1.59 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 154 or resid 156 through 503)) selection = (chain 'B' and (resid 27 through 154 or resid 156 through 503)) selection = (chain 'C' and (resid 27 through 154 or resid 156 through 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: 10.420 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- 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 : 4.47 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (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 ARG 0.004 0.000 ARG G 99 TYR 0.017 0.002 TYR B 135 PHE 0.014 0.002 PHE C 376 TRP 0.026 0.002 TRP H 119 HIS 0.006 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00325 (15939) covalent geometry : angle 0.64983 (21693) SS BOND : bond 0.00940 ( 15) SS BOND : angle 1.92051 ( 30) hydrogen bonds : bond 0.15861 ( 661) hydrogen bonds : angle 7.09458 ( 1830) link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 2.67911 ( 27) *********************** 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 : 0.674 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.7696 time to fit residues: 134.6405 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 350 ASN C 162 GLN C 350 ASN E 27 GLN D 27 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.184994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144026 restraints weight = 35414.740| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 5.73 r_work: 0.3197 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0604 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= 0.156 Angle : 0.620 6.738 21750 Z= 0.339 Chirality : 0.048 0.171 2598 Planarity : 0.004 0.037 2736 Dihedral : 5.962 58.425 2346 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.67 % Allowed : 4.43 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.18), residues: 1998 helix: 1.97 (0.26), residues: 408 sheet: 0.61 (0.21), residues: 582 loop : -1.01 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 61 TYR 0.017 0.002 TYR B 135 PHE 0.012 0.002 PHE H 80 TRP 0.012 0.001 TRP H 119 HIS 0.006 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00283 (15939) covalent geometry : angle 0.61024 (21693) SS BOND : bond 0.00859 ( 15) SS BOND : angle 1.82864 ( 30) hydrogen bonds : bond 0.06186 ( 661) hydrogen bonds : angle 5.95541 ( 1830) link_NAG-ASN : bond 0.00421 ( 9) link_NAG-ASN : angle 2.52733 ( 27) *********************** 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 164 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.620 Fit side-chains REVERT: F 50 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7462 (mtm110) outliers start: 12 outliers final: 8 residues processed: 156 average time/residue: 0.7521 time to fit residues: 127.4772 Evaluate side-chains 155 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 49 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 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 = 0.182451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139942 restraints weight = 38821.515| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 4.75 r_work: 0.3155 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 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 = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0808 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= 0.217 Angle : 0.731 7.342 21750 Z= 0.400 Chirality : 0.052 0.203 2598 Planarity : 0.005 0.039 2736 Dihedral : 6.094 51.828 2346 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.95 % Allowed : 7.18 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.18), residues: 1998 helix: 1.83 (0.26), residues: 408 sheet: 0.48 (0.20), residues: 582 loop : -1.08 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.021 0.002 TYR I 51 PHE 0.015 0.002 PHE C 376 TRP 0.016 0.002 TRP I 119 HIS 0.005 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00422 (15939) covalent geometry : angle 0.71928 (21693) SS BOND : bond 0.01119 ( 15) SS BOND : angle 2.18736 ( 30) hydrogen bonds : bond 0.07581 ( 661) hydrogen bonds : angle 6.16099 ( 1830) link_NAG-ASN : bond 0.00408 ( 9) link_NAG-ASN : angle 3.05469 ( 27) *********************** 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 165 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.559 Fit side-chains REVERT: A 139 LYS cc_start: 0.8240 (tppt) cc_final: 0.8027 (mmtt) outliers start: 17 outliers final: 12 residues processed: 156 average time/residue: 0.7478 time to fit residues: 126.5271 Evaluate side-chains 157 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 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 309 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 393 GLN 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 34 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 116 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.185933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143636 restraints weight = 38251.586| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 4.80 r_work: 0.3226 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15963 Z= 0.132 Angle : 0.566 6.086 21750 Z= 0.309 Chirality : 0.046 0.170 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.419 44.910 2346 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.01 % Allowed : 8.25 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 1998 helix: 2.11 (0.26), residues: 408 sheet: 0.59 (0.21), residues: 582 loop : -1.02 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.012 0.001 TYR C 275 PHE 0.010 0.001 PHE I 80 TRP 0.012 0.001 TRP G 48 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00234 (15939) covalent geometry : angle 0.55727 (21693) SS BOND : bond 0.00738 ( 15) SS BOND : angle 1.50631 ( 30) hydrogen bonds : bond 0.05407 ( 661) hydrogen bonds : angle 5.68714 ( 1830) link_NAG-ASN : bond 0.00378 ( 9) link_NAG-ASN : angle 2.48792 ( 27) *********************** 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 175 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.418 Fit side-chains REVERT: B 406 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7115 (pm20) outliers start: 18 outliers final: 8 residues processed: 166 average time/residue: 0.6829 time to fit residues: 123.2713 Evaluate side-chains 162 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 C 102 HIS C 162 GLN E 27 GLN D 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.182052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142500 restraints weight = 30064.302| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.74 r_work: 0.3152 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 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 = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15963 Z= 0.216 Angle : 0.722 7.619 21750 Z= 0.395 Chirality : 0.052 0.209 2598 Planarity : 0.005 0.036 2736 Dihedral : 5.772 43.554 2346 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.18 % Allowed : 8.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.18), residues: 1998 helix: 1.87 (0.25), residues: 408 sheet: 0.50 (0.20), residues: 582 loop : -1.09 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 61 TYR 0.021 0.002 TYR I 51 PHE 0.016 0.002 PHE C 376 TRP 0.014 0.002 TRP G 119 HIS 0.006 0.002 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00423 (15939) covalent geometry : angle 0.71099 (21693) SS BOND : bond 0.01077 ( 15) SS BOND : angle 2.05159 ( 30) hydrogen bonds : bond 0.07525 ( 661) hydrogen bonds : angle 6.05457 ( 1830) link_NAG-ASN : bond 0.00373 ( 9) link_NAG-ASN : angle 3.02522 ( 27) *********************** 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 166 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.619 Fit side-chains REVERT: A 139 LYS cc_start: 0.8239 (tppt) cc_final: 0.8010 (mmtt) REVERT: A 164 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6103 (p) REVERT: F 88 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7173 (pp30) REVERT: B 164 THR cc_start: 0.6344 (OUTLIER) cc_final: 0.6009 (t) REVERT: C 164 THR cc_start: 0.6576 (OUTLIER) cc_final: 0.6217 (p) REVERT: D 88 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6739 (pp30) outliers start: 21 outliers final: 10 residues processed: 158 average time/residue: 0.7261 time to fit residues: 124.4562 Evaluate side-chains 153 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 C residue 406 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 163 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 129 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** B 102 HIS C 102 HIS C 162 GLN E 27 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 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 = 0.4095 r_free = 0.4095 target = 0.186649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145413 restraints weight = 37384.165| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 5.94 r_work: 0.3232 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1086 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= 0.121 Angle : 0.539 6.412 21750 Z= 0.293 Chirality : 0.046 0.171 2598 Planarity : 0.004 0.033 2736 Dihedral : 5.003 38.028 2346 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.95 % Allowed : 9.32 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 1998 helix: 2.23 (0.26), residues: 408 sheet: 0.62 (0.20), residues: 612 loop : -1.03 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.013 0.001 TYR C 275 PHE 0.009 0.001 PHE I 80 TRP 0.012 0.001 TRP G 48 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00213 (15939) covalent geometry : angle 0.53098 (21693) SS BOND : bond 0.00652 ( 15) SS BOND : angle 1.39369 ( 30) hydrogen bonds : bond 0.04900 ( 661) hydrogen bonds : angle 5.50375 ( 1830) link_NAG-ASN : bond 0.00377 ( 9) link_NAG-ASN : angle 2.36325 ( 27) *********************** 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 168 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.550 Fit side-chains REVERT: A 164 THR cc_start: 0.6603 (OUTLIER) cc_final: 0.6189 (p) REVERT: B 164 THR cc_start: 0.6264 (OUTLIER) cc_final: 0.5986 (t) REVERT: B 406 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: C 164 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6181 (t) outliers start: 17 outliers final: 5 residues processed: 161 average time/residue: 0.6823 time to fit residues: 119.6031 Evaluate side-chains 158 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain G residue 127 VAL 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 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 59 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 147 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 C 102 HIS C 162 GLN E 27 GLN E 34 HIS D 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.182631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141188 restraints weight = 37083.219| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 5.93 r_work: 0.3168 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15963 Z= 0.203 Angle : 0.696 7.027 21750 Z= 0.380 Chirality : 0.051 0.205 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.485 42.031 2346 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.12 % Allowed : 9.43 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 1998 helix: 1.95 (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 ARG 0.005 0.001 ARG F 61 TYR 0.020 0.002 TYR I 51 PHE 0.015 0.002 PHE C 376 TRP 0.012 0.002 TRP G 119 HIS 0.008 0.002 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00393 (15939) covalent geometry : angle 0.68530 (21693) SS BOND : bond 0.01010 ( 15) SS BOND : angle 1.96296 ( 30) hydrogen bonds : bond 0.07205 ( 661) hydrogen bonds : angle 5.92273 ( 1830) link_NAG-ASN : bond 0.00356 ( 9) link_NAG-ASN : angle 2.88082 ( 27) *********************** 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 161 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.593 Fit side-chains REVERT: A 139 LYS cc_start: 0.8235 (tppt) cc_final: 0.8032 (mmtt) REVERT: A 164 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6275 (p) REVERT: B 164 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.5981 (t) REVERT: B 406 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: C 164 THR cc_start: 0.6559 (OUTLIER) cc_final: 0.6217 (p) REVERT: D 88 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6466 (pp30) outliers start: 20 outliers final: 8 residues processed: 153 average time/residue: 0.7284 time to fit residues: 120.7877 Evaluate side-chains 153 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 393 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 102 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 15 optimal weight: 0.0570 overall best weight: 1.5104 ------------------------------------------------------------------------------- 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 27 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4056 r_free = 0.4056 target = 0.183019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138749 restraints weight = 41773.498| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 5.00 r_work: 0.3181 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1035 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 : 0.650 6.727 21750 Z= 0.355 Chirality : 0.049 0.195 2598 Planarity : 0.004 0.035 2736 Dihedral : 5.404 42.321 2346 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.07 % Allowed : 9.48 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.18), residues: 1998 helix: 1.97 (0.26), residues: 408 sheet: 0.52 (0.20), residues: 582 loop : -1.08 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.018 0.002 TYR H 51 PHE 0.013 0.002 PHE C 376 TRP 0.010 0.001 TRP G 35 HIS 0.008 0.002 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00332 (15939) covalent geometry : angle 0.63962 (21693) SS BOND : bond 0.00916 ( 15) SS BOND : angle 1.80267 ( 30) hydrogen bonds : bond 0.06572 ( 661) hydrogen bonds : angle 5.85160 ( 1830) link_NAG-ASN : bond 0.00358 ( 9) link_NAG-ASN : angle 2.82298 ( 27) *********************** 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 161 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.557 Fit side-chains REVERT: A 164 THR cc_start: 0.6643 (OUTLIER) cc_final: 0.6258 (p) REVERT: B 164 THR cc_start: 0.6319 (OUTLIER) cc_final: 0.5994 (t) REVERT: B 406 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: C 164 THR cc_start: 0.6557 (OUTLIER) cc_final: 0.6208 (p) REVERT: D 88 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6477 (pp30) outliers start: 19 outliers final: 10 residues processed: 155 average time/residue: 0.7096 time to fit residues: 119.5194 Evaluate side-chains 157 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 393 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 H residue 75 THR Chi-restraints excluded: chain I residue 75 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 102 HIS C 162 GLN D 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128303 restraints weight = 43918.550| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.87 r_work: 0.3213 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1046 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= 0.152 Angle : 0.603 6.387 21750 Z= 0.329 Chirality : 0.048 0.184 2598 Planarity : 0.004 0.034 2736 Dihedral : 5.190 40.338 2346 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.12 % Allowed : 9.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 1998 helix: 2.08 (0.26), residues: 408 sheet: 0.54 (0.20), residues: 582 loop : -1.07 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.015 0.002 TYR H 51 PHE 0.012 0.002 PHE C 376 TRP 0.010 0.001 TRP G 48 HIS 0.008 0.002 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00277 (15939) covalent geometry : angle 0.59384 (21693) SS BOND : bond 0.00810 ( 15) SS BOND : angle 1.63595 ( 30) hydrogen bonds : bond 0.05962 ( 661) hydrogen bonds : angle 5.69804 ( 1830) link_NAG-ASN : bond 0.00362 ( 9) link_NAG-ASN : angle 2.62010 ( 27) *********************** 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 163 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.554 Fit side-chains REVERT: A 164 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.6067 (p) REVERT: A 406 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: B 164 THR cc_start: 0.6214 (OUTLIER) cc_final: 0.5878 (t) REVERT: B 406 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: C 164 THR cc_start: 0.6443 (OUTLIER) cc_final: 0.6000 (p) REVERT: D 88 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6560 (pp30) outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 0.7107 time to fit residues: 121.4572 Evaluate side-chains 160 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 48 optimal weight: 0.0070 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 34 HIS F 88 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.185225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143383 restraints weight = 37221.575| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.77 r_work: 0.3194 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1096 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 : 0.579 6.125 21750 Z= 0.315 Chirality : 0.047 0.181 2598 Planarity : 0.004 0.034 2736 Dihedral : 5.006 37.667 2346 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.12 % Allowed : 9.60 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.18), residues: 1998 helix: 2.18 (0.26), residues: 408 sheet: 0.55 (0.20), residues: 582 loop : -1.05 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.013 0.001 TYR B 135 PHE 0.011 0.001 PHE C 376 TRP 0.010 0.001 TRP G 48 HIS 0.008 0.002 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00255 (15939) covalent geometry : angle 0.57028 (21693) SS BOND : bond 0.00740 ( 15) SS BOND : angle 1.56100 ( 30) hydrogen bonds : bond 0.05617 ( 661) hydrogen bonds : angle 5.58891 ( 1830) link_NAG-ASN : bond 0.00361 ( 9) link_NAG-ASN : angle 2.47205 ( 27) ********************** 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 166 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.872 Fit side-chains REVERT: A 164 THR cc_start: 0.6589 (OUTLIER) cc_final: 0.6183 (p) REVERT: A 406 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: B 164 THR cc_start: 0.6337 (OUTLIER) cc_final: 0.6048 (t) REVERT: B 406 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: C 164 THR cc_start: 0.6604 (OUTLIER) cc_final: 0.6212 (p) REVERT: D 88 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6443 (pp30) outliers start: 20 outliers final: 12 residues processed: 160 average time/residue: 0.7018 time to fit residues: 122.3425 Evaluate side-chains 162 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** 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 = 0.4080 r_free = 0.4080 target = 0.185172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141711 restraints weight = 40467.662| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 5.09 r_work: 0.3196 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- 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: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 15963 Z= 0.171 Angle : 0.821 59.170 21750 Z= 0.467 Chirality : 0.051 0.916 2598 Planarity : 0.004 0.033 2736 Dihedral : 5.007 37.680 2346 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.07 % Allowed : 9.76 % Favored : 89.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 1998 helix: 2.18 (0.26), residues: 408 sheet: 0.56 (0.20), residues: 582 loop : -1.05 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.013 0.002 TYR H 51 PHE 0.011 0.002 PHE C 376 TRP 0.010 0.001 TRP G 48 HIS 0.010 0.002 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00311 (15939) covalent geometry : angle 0.81539 (21693) SS BOND : bond 0.00758 ( 15) SS BOND : angle 1.56772 ( 30) hydrogen bonds : bond 0.05675 ( 661) hydrogen bonds : angle 5.60542 ( 1830) link_NAG-ASN : bond 0.00364 ( 9) link_NAG-ASN : angle 2.47637 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7627.14 seconds wall clock time: 130 minutes 8.62 seconds (7808.62 seconds total)