Starting phenix.real_space_refine on Fri Mar 15 07:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcy_0199/03_2024/6hcy_0199_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 18 5.49 5 S 51 5.16 5 C 7209 2.51 5 N 1800 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11007 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.22, per 1000 atoms: 0.57 Number of scatterers: 11007 At special positions: 0 Unit cell: (92.6478, 95.0859, 116.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 51 16.00 P 18 15.00 O 1926 8.00 N 1800 7.00 C 7209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied NAG-ASN " NAG A 504 " - " ASN A 323 " " NAG B 504 " - " ASN B 323 " " NAG C 504 " - " ASN C 323 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 2.0 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 6 sheets defined 55.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'C' and resid 29 through 41 removed outlier: 3.532A pdb=" N GLN C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.848A pdb=" N LYS C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.641A pdb=" N THR C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 160 through 172 removed outlier: 3.509A pdb=" N ARG C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.822A pdb=" N LYS C 187 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 188 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 189 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 201 through 222 removed outlier: 3.708A pdb=" N PHE C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 221 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 228 No H-bonds generated for 'chain 'C' and resid 225 through 228' Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 243 through 256 Proline residue: C 248 - end of helix Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.516A pdb=" N ALA C 266 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 315 through 330 Processing helix chain 'C' and resid 339 through 365 removed outlier: 4.078A pdb=" N VAL C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 385 through 403 removed outlier: 3.554A pdb=" N LEU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 398 " --> pdb=" O CYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.593A pdb=" N ASN C 444 " --> pdb=" O PRO C 440 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.532A pdb=" N GLN A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.849A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.641A pdb=" N THR A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.509A pdb=" N ARG A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.822A pdb=" N LYS A 187 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 189 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 222 removed outlier: 3.707A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 243 through 256 Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.516A pdb=" N ALA A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 339 through 365 removed outlier: 4.078A pdb=" N VAL A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 385 through 403 removed outlier: 3.555A pdb=" N LEU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 438 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.593A pdb=" N ASN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.532A pdb=" N GLN B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.849A pdb=" N LYS B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.641A pdb=" N THR B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 160 through 172 removed outlier: 3.509A pdb=" N ARG B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.822A pdb=" N LYS B 187 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 188 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 190 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 201 through 222 removed outlier: 3.709A pdb=" N PHE B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 243 through 256 Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.516A pdb=" N ALA B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 339 through 365 removed outlier: 4.077A pdb=" N VAL B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.554A pdb=" N LEU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 438 Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.593A pdb=" N ASN B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.253A pdb=" N ILE C 76 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE C 25 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 78 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE C 100 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 79 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 102 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS C 129 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP C 103 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 131 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 152 through 155 removed outlier: 6.272A pdb=" N THR C 176 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 155 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET C 178 " --> pdb=" O VAL C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.253A pdb=" N ILE A 76 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE A 25 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 78 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 100 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 79 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 102 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS A 129 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP A 103 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 131 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 152 through 155 removed outlier: 6.272A pdb=" N THR A 176 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 155 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET A 178 " --> pdb=" O VAL A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.253A pdb=" N ILE B 76 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 25 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 78 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE B 100 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 79 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 102 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS B 129 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 103 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 131 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 152 through 155 removed outlier: 6.272A pdb=" N THR B 176 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 155 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET B 178 " --> pdb=" O VAL B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 411 hydrogen bonds defined for protein. 1188 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: 2.68 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3496 1.36 - 1.55: 7702 1.55 - 1.73: 40 1.73 - 1.91: 78 1.91 - 2.10: 9 Bond restraints: 11325 Sorted by residual: bond pdb=" C1D NAP B 501 " pdb=" C2D NAP B 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP A 501 " pdb=" C2D NAP A 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP C 501 " pdb=" C2D NAP C 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1D NAP B 501 " pdb=" O4D NAP B 501 " ideal model delta sigma weight residual 1.375 1.611 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1D NAP C 501 " pdb=" O4D NAP C 501 " ideal model delta sigma weight residual 1.375 1.610 -0.235 2.00e-02 2.50e+03 1.39e+02 ... (remaining 11320 not shown) Histogram of bond angle deviations from ideal: 86.47 - 104.87: 226 104.87 - 123.26: 14706 123.26 - 141.66: 560 141.66 - 160.05: 0 160.05 - 178.45: 6 Bond angle restraints: 15498 Sorted by residual: angle pdb=" CB ARG A 290 " pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" CB ARG C 290 " pdb=" CG ARG C 290 " pdb=" CD ARG C 290 " ideal model delta sigma weight residual 111.30 100.18 11.12 2.30e+00 1.89e-01 2.34e+01 angle pdb=" CB ARG B 290 " pdb=" CG ARG B 290 " pdb=" CD ARG B 290 " ideal model delta sigma weight residual 111.30 100.20 11.10 2.30e+00 1.89e-01 2.33e+01 angle pdb=" O1N NAP B 501 " pdb=" PN NAP B 501 " pdb=" O2N NAP B 501 " ideal model delta sigma weight residual 122.51 109.02 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" O1N NAP C 501 " pdb=" PN NAP C 501 " pdb=" O2N NAP C 501 " ideal model delta sigma weight residual 122.51 109.03 13.48 3.00e+00 1.11e-01 2.02e+01 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 6537 34.81 - 69.63: 204 69.63 - 104.44: 33 104.44 - 139.25: 0 139.25 - 174.06: 3 Dihedral angle restraints: 6777 sinusoidal: 2952 harmonic: 3825 Sorted by residual: dihedral pdb=" C2C HEM A 502 " pdb=" C3C HEM A 502 " pdb=" CAC HEM A 502 " pdb=" CBC HEM A 502 " ideal model delta sinusoidal sigma weight residual -0.00 -80.33 80.33 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2C HEM C 502 " pdb=" C3C HEM C 502 " pdb=" CAC HEM C 502 " pdb=" CBC HEM C 502 " ideal model delta sinusoidal sigma weight residual 0.00 -80.30 80.30 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2C HEM B 502 " pdb=" C3C HEM B 502 " pdb=" CAC HEM B 502 " pdb=" CBC HEM B 502 " ideal model delta sinusoidal sigma weight residual 0.00 -80.25 80.25 2 1.00e+01 1.00e-02 4.66e+01 ... (remaining 6774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1384 0.071 - 0.142: 300 0.142 - 0.214: 48 0.214 - 0.285: 5 0.285 - 0.356: 6 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C2B NAP B 501 " pdb=" C1B NAP B 501 " pdb=" C3B NAP B 501 " pdb=" O2B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2B NAP C 501 " pdb=" C1B NAP C 501 " pdb=" C3B NAP C 501 " pdb=" O2B NAP C 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1740 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 286 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP B 286 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 286 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 286 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 286 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 286 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 286 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 286 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 286 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 286 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP C 286 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 286 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 286 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 286 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 286 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 286 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 286 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 286 " -0.004 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 49 2.59 - 3.17: 8727 3.17 - 3.75: 16777 3.75 - 4.32: 24605 4.32 - 4.90: 39678 Nonbonded interactions: 89836 Sorted by model distance: nonbonded pdb=" NE2 HIS A 304 " pdb="FE HEM A 502 " model vdw 2.017 3.080 nonbonded pdb=" NE2 HIS C 304 " pdb="FE HEM C 502 " model vdw 2.018 3.080 nonbonded pdb=" NE2 HIS B 304 " pdb="FE HEM B 502 " model vdw 2.018 3.080 nonbonded pdb=" O3' FAD B 503 " pdb=" O5' FAD B 503 " model vdw 2.260 2.440 nonbonded pdb=" O3' FAD C 503 " pdb=" O5' FAD C 503 " model vdw 2.260 2.440 ... (remaining 89831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=1.00 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.710 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.770 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.015 0.237 11325 Z= 0.906 Angle : 1.262 13.491 15498 Z= 0.590 Chirality : 0.065 0.356 1743 Planarity : 0.008 0.058 1839 Dihedral : 16.874 174.064 4323 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.79 % Allowed : 5.28 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.30 (0.15), residues: 1302 helix: -4.31 (0.07), residues: 846 sheet: -1.97 (0.42), residues: 141 loop : -3.85 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP B 286 HIS 0.010 0.002 HIS A 85 PHE 0.017 0.003 PHE A 302 TYR 0.021 0.002 TYR A 348 ARG 0.012 0.001 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 1.242 Fit side-chains REVERT: C 119 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8327 (mt-10) REVERT: C 147 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8522 (pp) REVERT: C 151 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8179 (ttm-80) REVERT: C 161 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8795 (ttpp) REVERT: C 184 MET cc_start: 0.8550 (mmp) cc_final: 0.8333 (ptp) REVERT: C 191 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8232 (ttmm) REVERT: C 231 LYS cc_start: 0.8502 (mttt) cc_final: 0.7989 (tmtt) REVERT: C 281 ASP cc_start: 0.8594 (t0) cc_final: 0.8184 (t0) REVERT: C 450 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7831 (mtp180) REVERT: A 20 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7833 (tp30) REVERT: A 87 ASP cc_start: 0.8600 (m-30) cc_final: 0.8389 (m-30) REVERT: A 119 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8322 (mt-10) REVERT: A 147 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8595 (pp) REVERT: A 159 ASP cc_start: 0.8080 (t0) cc_final: 0.7800 (t0) REVERT: A 161 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8732 (ttpp) REVERT: A 184 MET cc_start: 0.8581 (mmp) cc_final: 0.8105 (ptp) REVERT: A 231 LYS cc_start: 0.8458 (mttt) cc_final: 0.8082 (tmtt) REVERT: A 281 ASP cc_start: 0.8822 (t0) cc_final: 0.8392 (t0) REVERT: B 38 MET cc_start: 0.8885 (mtt) cc_final: 0.8674 (mtt) REVERT: B 115 GLU cc_start: 0.8002 (pm20) cc_final: 0.7733 (pm20) REVERT: B 119 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8273 (mt-10) REVERT: B 147 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B 151 ARG cc_start: 0.8447 (tpp80) cc_final: 0.8091 (tpp-160) REVERT: B 184 MET cc_start: 0.8539 (mmp) cc_final: 0.8335 (ptp) REVERT: B 188 GLU cc_start: 0.7912 (tt0) cc_final: 0.7694 (tm-30) REVERT: B 191 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8371 (ttmm) REVERT: B 217 TYR cc_start: 0.9068 (t80) cc_final: 0.8799 (t80) REVERT: B 231 LYS cc_start: 0.8493 (mttt) cc_final: 0.8018 (tmtt) REVERT: B 281 ASP cc_start: 0.8525 (t0) cc_final: 0.8140 (t0) outliers start: 9 outliers final: 0 residues processed: 231 average time/residue: 0.3148 time to fit residues: 94.9945 Evaluate side-chains 117 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN C 143 GLN C 234 ASN C 372 ASN A 234 ASN A 372 ASN B 111 ASN B 234 ASN B 372 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11325 Z= 0.250 Angle : 0.680 10.347 15498 Z= 0.315 Chirality : 0.044 0.136 1743 Planarity : 0.006 0.042 1839 Dihedral : 17.114 169.657 1914 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.52 % Allowed : 7.48 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.20), residues: 1302 helix: -2.08 (0.15), residues: 828 sheet: -1.54 (0.43), residues: 141 loop : -3.19 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 286 HIS 0.003 0.001 HIS B 85 PHE 0.009 0.001 PHE C 300 TYR 0.017 0.001 TYR A 415 ARG 0.007 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.190 Fit side-chains REVERT: C 147 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8434 (pp) REVERT: C 151 ARG cc_start: 0.8423 (tpp80) cc_final: 0.7935 (ttm-80) REVERT: C 161 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8705 (mtpp) REVERT: C 231 LYS cc_start: 0.8453 (mttt) cc_final: 0.8024 (tmtt) REVERT: C 281 ASP cc_start: 0.8542 (t0) cc_final: 0.8215 (t0) REVERT: C 416 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (pp) REVERT: C 450 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7850 (mtp180) REVERT: A 147 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8379 (pp) REVERT: A 161 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8484 (ttpp) REVERT: A 184 MET cc_start: 0.8571 (mmp) cc_final: 0.8199 (ptp) REVERT: A 199 MET cc_start: 0.9134 (mmm) cc_final: 0.8902 (mmm) REVERT: A 231 LYS cc_start: 0.8402 (mttt) cc_final: 0.8135 (tmtt) REVERT: A 281 ASP cc_start: 0.8750 (t0) cc_final: 0.8302 (t0) REVERT: A 453 TRP cc_start: 0.7567 (t-100) cc_final: 0.7337 (t-100) REVERT: B 119 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8230 (mt-10) REVERT: B 147 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8428 (pp) REVERT: B 151 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8188 (ttm-80) REVERT: B 191 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8261 (ttmm) REVERT: B 231 LYS cc_start: 0.8453 (mttt) cc_final: 0.8024 (tmtt) REVERT: B 281 ASP cc_start: 0.8527 (t0) cc_final: 0.8102 (t0) REVERT: B 448 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7473 (ttp-110) outliers start: 40 outliers final: 19 residues processed: 161 average time/residue: 0.2751 time to fit residues: 59.6543 Evaluate side-chains 129 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 94 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN A 85 HIS A 372 ASN B 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11325 Z= 0.198 Angle : 0.607 7.989 15498 Z= 0.277 Chirality : 0.042 0.122 1743 Planarity : 0.004 0.036 1839 Dihedral : 14.893 168.524 1914 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.52 % Allowed : 8.18 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.23), residues: 1302 helix: -0.60 (0.17), residues: 831 sheet: -1.27 (0.43), residues: 135 loop : -2.83 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 286 HIS 0.003 0.001 HIS B 397 PHE 0.009 0.001 PHE B 300 TYR 0.015 0.001 TYR C 348 ARG 0.005 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8495 (pp) REVERT: C 151 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8080 (ttm-80) REVERT: C 231 LYS cc_start: 0.8440 (mttt) cc_final: 0.8008 (tmtt) REVERT: C 281 ASP cc_start: 0.8424 (t0) cc_final: 0.8109 (t0) REVERT: C 416 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8164 (pp) REVERT: C 450 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7819 (mtp180) REVERT: A 39 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 147 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8343 (pp) REVERT: A 161 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8553 (mtpp) REVERT: A 184 MET cc_start: 0.8508 (mmp) cc_final: 0.8224 (ptp) REVERT: A 199 MET cc_start: 0.9124 (mmm) cc_final: 0.8901 (mmm) REVERT: A 231 LYS cc_start: 0.8371 (mttt) cc_final: 0.8098 (tmtt) REVERT: A 281 ASP cc_start: 0.8611 (t0) cc_final: 0.8176 (t0) REVERT: B 119 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8245 (mt-10) REVERT: B 147 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8417 (pp) REVERT: B 151 ARG cc_start: 0.8389 (tpp80) cc_final: 0.8150 (ttm-80) REVERT: B 161 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8514 (mtpp) REVERT: B 188 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 231 LYS cc_start: 0.8456 (mttt) cc_final: 0.8046 (tmtt) REVERT: B 281 ASP cc_start: 0.8411 (t0) cc_final: 0.8150 (t0) outliers start: 40 outliers final: 19 residues processed: 149 average time/residue: 0.2623 time to fit residues: 53.3277 Evaluate side-chains 124 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0980 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 ASN A 111 ASN B 111 ASN B 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11325 Z= 0.292 Angle : 0.620 8.619 15498 Z= 0.283 Chirality : 0.044 0.127 1743 Planarity : 0.004 0.035 1839 Dihedral : 13.730 168.464 1914 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.31 % Allowed : 7.39 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1302 helix: 0.09 (0.18), residues: 825 sheet: -0.99 (0.44), residues: 135 loop : -2.58 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 286 HIS 0.005 0.001 HIS B 397 PHE 0.010 0.001 PHE A 302 TYR 0.015 0.001 TYR C 348 ARG 0.005 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 97 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8568 (pp) REVERT: C 231 LYS cc_start: 0.8445 (mttt) cc_final: 0.8029 (tmtt) REVERT: C 281 ASP cc_start: 0.8495 (t0) cc_final: 0.8184 (t0) REVERT: C 416 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (pp) REVERT: C 450 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7788 (mtp180) REVERT: A 39 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (mm) REVERT: A 147 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8277 (pp) REVERT: A 161 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8514 (mtpp) REVERT: A 184 MET cc_start: 0.8524 (mmp) cc_final: 0.8221 (ptp) REVERT: A 231 LYS cc_start: 0.8403 (mttt) cc_final: 0.8112 (tmtt) REVERT: A 281 ASP cc_start: 0.8609 (t0) cc_final: 0.8233 (t0) REVERT: A 415 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: B 119 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8249 (mt-10) REVERT: B 147 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8145 (pp) REVERT: B 151 ARG cc_start: 0.8386 (tpp80) cc_final: 0.8019 (ttm-80) REVERT: B 161 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8539 (mtpp) REVERT: B 188 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7103 (tm-30) REVERT: B 231 LYS cc_start: 0.8455 (mttt) cc_final: 0.8023 (tmtt) REVERT: B 278 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8226 (mtp-110) REVERT: B 281 ASP cc_start: 0.8519 (t0) cc_final: 0.8151 (t0) REVERT: B 290 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7848 (mtm110) REVERT: B 292 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8472 (mm110) outliers start: 49 outliers final: 26 residues processed: 139 average time/residue: 0.2894 time to fit residues: 54.4908 Evaluate side-chains 129 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 11325 Z= 0.440 Angle : 0.680 9.812 15498 Z= 0.311 Chirality : 0.047 0.149 1743 Planarity : 0.004 0.036 1839 Dihedral : 13.612 167.142 1914 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.22 % Allowed : 8.27 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1302 helix: 0.34 (0.18), residues: 828 sheet: -0.57 (0.46), residues: 117 loop : -2.39 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 286 HIS 0.006 0.001 HIS B 397 PHE 0.011 0.002 PHE C 302 TYR 0.025 0.002 TYR B 415 ARG 0.004 0.001 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8509 (pp) REVERT: C 231 LYS cc_start: 0.8461 (mttt) cc_final: 0.7962 (tmtt) REVERT: C 281 ASP cc_start: 0.8605 (t0) cc_final: 0.8208 (t0) REVERT: C 416 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 450 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7918 (mtp85) REVERT: A 39 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 147 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 161 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8532 (mtpp) REVERT: A 184 MET cc_start: 0.8517 (mmp) cc_final: 0.8268 (ptp) REVERT: A 231 LYS cc_start: 0.8424 (mttt) cc_final: 0.8053 (tmtt) REVERT: A 281 ASP cc_start: 0.8704 (t0) cc_final: 0.8299 (t0) REVERT: A 415 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7546 (m-10) REVERT: B 119 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8287 (mt-10) REVERT: B 147 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8163 (pp) REVERT: B 151 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8135 (ttm-80) REVERT: B 161 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8541 (mtpp) REVERT: B 188 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7149 (tm-30) REVERT: B 231 LYS cc_start: 0.8492 (mttt) cc_final: 0.7998 (tmtt) REVERT: B 278 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8315 (mtp-110) REVERT: B 281 ASP cc_start: 0.8675 (t0) cc_final: 0.8341 (t0) REVERT: B 290 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8253 (mtm180) REVERT: B 292 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8344 (mm110) REVERT: B 415 TYR cc_start: 0.8157 (m-10) cc_final: 0.7954 (m-10) outliers start: 48 outliers final: 24 residues processed: 135 average time/residue: 0.2735 time to fit residues: 50.1796 Evaluate side-chains 122 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 65 optimal weight: 0.0670 chunk 120 optimal weight: 0.5980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11325 Z= 0.159 Angle : 0.568 8.796 15498 Z= 0.257 Chirality : 0.041 0.122 1743 Planarity : 0.004 0.036 1839 Dihedral : 13.019 167.594 1914 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.78 % Allowed : 8.71 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1302 helix: 0.65 (0.19), residues: 849 sheet: -0.39 (0.48), residues: 117 loop : -2.33 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 286 HIS 0.003 0.000 HIS B 85 PHE 0.009 0.001 PHE B 300 TYR 0.017 0.001 TYR C 348 ARG 0.003 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: C 147 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 231 LYS cc_start: 0.8489 (mttt) cc_final: 0.8034 (tmtt) REVERT: C 281 ASP cc_start: 0.8428 (t0) cc_final: 0.8079 (t0) REVERT: C 450 ARG cc_start: 0.8231 (mtm110) cc_final: 0.7838 (mtp85) REVERT: A 39 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8536 (mm) REVERT: A 147 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8418 (pp) REVERT: A 161 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8470 (mtpp) REVERT: A 184 MET cc_start: 0.8488 (mmp) cc_final: 0.8257 (ptp) REVERT: A 231 LYS cc_start: 0.8446 (mttt) cc_final: 0.8085 (tmtt) REVERT: A 281 ASP cc_start: 0.8497 (t0) cc_final: 0.8042 (t0) REVERT: A 415 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7406 (m-10) REVERT: A 448 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7419 (ttp80) REVERT: B 147 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8283 (pp) REVERT: B 161 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8449 (mtpp) REVERT: B 188 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7135 (tm-30) REVERT: B 231 LYS cc_start: 0.8462 (mttt) cc_final: 0.7972 (tmtt) REVERT: B 278 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8297 (mtp-110) REVERT: B 281 ASP cc_start: 0.8452 (t0) cc_final: 0.8087 (t0) REVERT: B 290 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8215 (mtm180) outliers start: 43 outliers final: 28 residues processed: 134 average time/residue: 0.2718 time to fit residues: 50.0436 Evaluate side-chains 122 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 415 TYR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11325 Z= 0.177 Angle : 0.561 7.704 15498 Z= 0.255 Chirality : 0.041 0.120 1743 Planarity : 0.004 0.034 1839 Dihedral : 12.886 167.805 1914 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.61 % Allowed : 9.67 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1302 helix: 0.86 (0.19), residues: 849 sheet: -0.26 (0.48), residues: 117 loop : -2.23 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 453 HIS 0.003 0.000 HIS B 85 PHE 0.007 0.001 PHE B 300 TYR 0.016 0.001 TYR C 348 ARG 0.003 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 91 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: C 147 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8659 (pp) REVERT: C 231 LYS cc_start: 0.8491 (mttt) cc_final: 0.8040 (tmtt) REVERT: C 281 ASP cc_start: 0.8401 (t0) cc_final: 0.8078 (t0) REVERT: C 405 ARG cc_start: 0.6827 (mmt90) cc_final: 0.6574 (mpt-90) REVERT: C 450 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7777 (mtp85) REVERT: A 39 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 147 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8432 (pp) REVERT: A 161 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8489 (mtpp) REVERT: A 184 MET cc_start: 0.8478 (mmp) cc_final: 0.8244 (ptp) REVERT: A 231 LYS cc_start: 0.8428 (mttt) cc_final: 0.8049 (tmtt) REVERT: A 281 ASP cc_start: 0.8450 (t0) cc_final: 0.8047 (t0) REVERT: A 415 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.7433 (m-10) REVERT: B 147 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8312 (pp) REVERT: B 161 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8438 (mtpp) REVERT: B 188 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 231 LYS cc_start: 0.8461 (mttt) cc_final: 0.7979 (tmtt) REVERT: B 281 ASP cc_start: 0.8395 (t0) cc_final: 0.8070 (t0) REVERT: B 290 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8179 (mtm180) outliers start: 41 outliers final: 30 residues processed: 125 average time/residue: 0.2711 time to fit residues: 46.6145 Evaluate side-chains 122 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 415 TYR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11325 Z= 0.243 Angle : 0.584 7.652 15498 Z= 0.264 Chirality : 0.042 0.125 1743 Planarity : 0.004 0.033 1839 Dihedral : 12.905 167.782 1914 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.43 % Allowed : 10.29 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1302 helix: 0.96 (0.19), residues: 849 sheet: -0.16 (0.48), residues: 117 loop : -2.18 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 286 HIS 0.004 0.001 HIS C 397 PHE 0.008 0.001 PHE A 359 TYR 0.016 0.001 TYR A 348 ARG 0.003 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: C 147 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (pp) REVERT: C 231 LYS cc_start: 0.8511 (mttt) cc_final: 0.8021 (tmtt) REVERT: C 281 ASP cc_start: 0.8421 (t0) cc_final: 0.8081 (t0) REVERT: C 405 ARG cc_start: 0.6854 (mmt90) cc_final: 0.6614 (mpt-90) REVERT: C 450 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7745 (mtp85) REVERT: A 39 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 147 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8483 (pp) REVERT: A 161 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8496 (mtpp) REVERT: A 184 MET cc_start: 0.8505 (mmp) cc_final: 0.8277 (ptp) REVERT: A 231 LYS cc_start: 0.8440 (mttt) cc_final: 0.8074 (tmtt) REVERT: A 281 ASP cc_start: 0.8462 (t0) cc_final: 0.8055 (t0) REVERT: A 415 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: B 147 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8293 (pp) REVERT: B 161 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8447 (mtpp) REVERT: B 188 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 231 LYS cc_start: 0.8461 (mttt) cc_final: 0.7998 (tmtt) REVERT: B 281 ASP cc_start: 0.8458 (t0) cc_final: 0.8121 (t0) REVERT: B 290 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8236 (mtm180) outliers start: 39 outliers final: 28 residues processed: 120 average time/residue: 0.2783 time to fit residues: 45.6822 Evaluate side-chains 120 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 415 TYR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.4980 chunk 115 optimal weight: 0.0070 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11325 Z= 0.171 Angle : 0.551 6.787 15498 Z= 0.250 Chirality : 0.041 0.139 1743 Planarity : 0.003 0.032 1839 Dihedral : 12.661 168.121 1914 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.17 % Allowed : 10.99 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1302 helix: 1.13 (0.19), residues: 852 sheet: -0.08 (0.49), residues: 117 loop : -2.09 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 282 HIS 0.003 0.000 HIS B 85 PHE 0.006 0.001 PHE A 300 TYR 0.016 0.001 TYR C 348 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: C 231 LYS cc_start: 0.8482 (mttt) cc_final: 0.8041 (tmtt) REVERT: C 281 ASP cc_start: 0.8278 (t0) cc_final: 0.7972 (t0) REVERT: C 405 ARG cc_start: 0.6750 (mmt90) cc_final: 0.6469 (mpt90) REVERT: C 450 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7658 (mtp85) REVERT: A 39 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8518 (mm) REVERT: A 147 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8484 (pp) REVERT: A 161 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8481 (mtpp) REVERT: A 231 LYS cc_start: 0.8418 (mttt) cc_final: 0.8052 (tmtt) REVERT: A 281 ASP cc_start: 0.8348 (t0) cc_final: 0.7927 (t0) REVERT: B 20 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: B 147 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8439 (pp) REVERT: B 161 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8394 (mtpp) REVERT: B 188 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 217 TYR cc_start: 0.8906 (t80) cc_final: 0.8588 (t80) REVERT: B 231 LYS cc_start: 0.8472 (mttt) cc_final: 0.7938 (tmtt) REVERT: B 281 ASP cc_start: 0.8299 (t0) cc_final: 0.7933 (t0) REVERT: B 290 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8142 (mpp80) outliers start: 36 outliers final: 23 residues processed: 120 average time/residue: 0.2779 time to fit residues: 46.0499 Evaluate side-chains 116 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11325 Z= 0.369 Angle : 0.639 9.125 15498 Z= 0.288 Chirality : 0.046 0.151 1743 Planarity : 0.004 0.032 1839 Dihedral : 12.990 168.298 1912 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.17 % Allowed : 11.17 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1302 helix: 0.96 (0.19), residues: 855 sheet: -0.10 (0.48), residues: 117 loop : -2.11 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 286 HIS 0.005 0.001 HIS A 397 PHE 0.012 0.001 PHE A 359 TYR 0.016 0.001 TYR B 348 ARG 0.003 0.000 ARG B 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: C 147 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8660 (pp) REVERT: C 231 LYS cc_start: 0.8511 (mttt) cc_final: 0.8004 (tmtt) REVERT: C 281 ASP cc_start: 0.8514 (t0) cc_final: 0.8199 (t0) REVERT: C 405 ARG cc_start: 0.6739 (mmt90) cc_final: 0.6484 (mpt90) REVERT: C 450 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7707 (mtp85) REVERT: A 39 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 147 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8490 (pp) REVERT: A 161 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8511 (mtpp) REVERT: A 231 LYS cc_start: 0.8457 (mttt) cc_final: 0.8037 (tmtt) REVERT: A 281 ASP cc_start: 0.8541 (t0) cc_final: 0.8132 (t0) REVERT: B 147 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8362 (pp) REVERT: B 161 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8461 (mtpp) REVERT: B 188 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 231 LYS cc_start: 0.8524 (mttt) cc_final: 0.7998 (tmtt) REVERT: B 281 ASP cc_start: 0.8537 (t0) cc_final: 0.8180 (t0) REVERT: B 290 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7716 (mtm110) outliers start: 36 outliers final: 26 residues processed: 117 average time/residue: 0.2835 time to fit residues: 45.4657 Evaluate side-chains 115 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 414 TRP Chi-restraints excluded: chain C residue 415 TYR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 0.0030 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.078020 restraints weight = 14089.287| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.91 r_work: 0.2634 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11325 Z= 0.210 Angle : 0.579 7.650 15498 Z= 0.260 Chirality : 0.042 0.156 1743 Planarity : 0.004 0.031 1839 Dihedral : 12.797 167.933 1912 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.17 % Allowed : 11.08 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1302 helix: 0.94 (0.19), residues: 873 sheet: -0.06 (0.49), residues: 117 loop : -2.24 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 286 HIS 0.003 0.000 HIS B 85 PHE 0.007 0.001 PHE A 359 TYR 0.016 0.001 TYR A 415 ARG 0.003 0.000 ARG B 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.74 seconds wall clock time: 43 minutes 23.03 seconds (2603.03 seconds total)