Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 23:56:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/04_2023/7ph4_13406_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.118 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: 7 Type Number sf(0) Gaussians Gd 2 15.26 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 6826 2.51 5 N 1878 2.21 5 O 2068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 530": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10846 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4469 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 13, 'TRANS': 562} Chain: "B" Number of atoms: 4469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4469 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 13, 'TRANS': 562} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 847 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 847 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' MG': 1, 'ANP': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' MG': 1, 'ANP': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Ad-hoc single atom residues: {' GD': 1} Unusual residues: {'88T': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Ad-hoc single atom residues: {' GD': 1} Unusual residues: {'88T': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C10 88T C 200 " occ=0.09 ... (35 atoms not shown) pdb=" O9 88T C 200 " occ=0.09 residue: pdb=" C10 88T D 200 " occ=0.09 ... (35 atoms not shown) pdb=" O9 88T D 200 " occ=0.09 Time building chain proxies: 6.35, per 1000 atoms: 0.59 Number of scatterers: 10846 At special positions: 0 Unit cell: (77.841, 97.092, 156.519, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Gd 2 63.96 S 64 16.00 P 6 15.00 Mg 2 11.99 O 2068 8.00 N 1878 7.00 C 6826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 54.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 52 Proline residue: A 18 - end of helix Proline residue: A 22 - end of helix removed outlier: 5.788A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 62 through 110 removed outlier: 3.739A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.571A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 163 removed outlier: 3.912A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 212 removed outlier: 5.113A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 223 through 270 Proline residue: A 253 - end of helix removed outlier: 3.929A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 323 removed outlier: 4.130A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.191A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.865A pdb=" N GLN A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 513 through 526 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'B' and resid 9 through 52 Proline residue: B 18 - end of helix Proline residue: B 22 - end of helix removed outlier: 5.788A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY B 26 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 62 through 110 removed outlier: 3.739A pdb=" N TRP B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.571A pdb=" N LYS B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 163 removed outlier: 3.911A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 212 removed outlier: 5.114A pdb=" N ILE B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 223 through 270 Proline residue: B 253 - end of helix removed outlier: 3.930A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 323 removed outlier: 4.115A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.936A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 412 through 418 removed outlier: 3.865A pdb=" N GLN B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 No H-bonds generated for 'chain 'B' and resid 434 through 437' Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 513 through 526 Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 399 through 402 removed outlier: 4.969A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 555 through 560 removed outlier: 6.843A pdb=" N VAL A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 559 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER A 532 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 374 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 534 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY A 376 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 399 through 402 removed outlier: 4.969A pdb=" N ILE B 362 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 555 through 560 removed outlier: 6.842A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER B 532 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU B 374 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 534 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY B 376 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= F, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.063A pdb=" N ARG C 38 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= H, first strand: chain 'D' and resid 108 through 110 removed outlier: 6.062A pdb=" N ARG D 38 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.76: 10892 1.76 - 2.37: 118 2.37 - 2.98: 0 2.98 - 3.60: 0 3.60 - 4.21: 2 Bond restraints: 11012 Sorted by residual: bond pdb=" O6 88T D 200 " pdb=" O9 88T D 200 " ideal model delta sigma weight residual 1.419 4.212 -2.793 2.00e-02 2.50e+03 1.95e+04 bond pdb=" O6 88T C 200 " pdb=" O9 88T C 200 " ideal model delta sigma weight residual 1.419 4.211 -2.792 2.00e-02 2.50e+03 1.95e+04 bond pdb=" C11 88T D 200 " pdb=" N4 88T D 200 " ideal model delta sigma weight residual 1.837 1.507 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" C11 88T C 200 " pdb=" N4 88T C 200 " ideal model delta sigma weight residual 1.837 1.508 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" C12 88T C 200 " pdb=" N4 88T C 200 " ideal model delta sigma weight residual 1.814 1.494 0.320 2.00e-02 2.50e+03 2.56e+02 ... (remaining 11007 not shown) Histogram of bond angle deviations from ideal: 34.59 - 57.67: 2 57.67 - 80.76: 0 80.76 - 103.84: 152 103.84 - 126.92: 14632 126.92 - 150.01: 110 Bond angle restraints: 14896 Sorted by residual: angle pdb=" C15 88T C 200 " pdb=" O6 88T C 200 " pdb=" O9 88T C 200 " ideal model delta sigma weight residual 109.36 34.59 74.77 3.00e+00 1.11e-01 6.21e+02 angle pdb=" C15 88T D 200 " pdb=" O6 88T D 200 " pdb=" O9 88T D 200 " ideal model delta sigma weight residual 109.36 34.60 74.76 3.00e+00 1.11e-01 6.21e+02 angle pdb=" C10 88T C 200 " pdb=" O4 88T C 200 " pdb=" O8 88T C 200 " ideal model delta sigma weight residual 109.57 150.01 -40.44 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C10 88T D 200 " pdb=" O4 88T D 200 " pdb=" O8 88T D 200 " ideal model delta sigma weight residual 109.57 149.95 -40.38 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C21 88T C 200 " pdb=" O8 88T C 200 " pdb=" O4 88T C 200 " ideal model delta sigma weight residual 105.77 137.57 -31.80 3.00e+00 1.11e-01 1.12e+02 ... (remaining 14891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 6479 35.69 - 71.37: 123 71.37 - 107.06: 12 107.06 - 142.74: 6 142.74 - 178.43: 4 Dihedral angle restraints: 6624 sinusoidal: 2656 harmonic: 3968 Sorted by residual: dihedral pdb=" C ARG A 14 " pdb=" N ARG A 14 " pdb=" CA ARG A 14 " pdb=" CB ARG A 14 " ideal model delta harmonic sigma weight residual -122.60 -138.65 16.05 0 2.50e+00 1.60e-01 4.12e+01 dihedral pdb=" N ARG A 14 " pdb=" C ARG A 14 " pdb=" CA ARG A 14 " pdb=" CB ARG A 14 " ideal model delta harmonic sigma weight residual 122.80 138.11 -15.31 0 2.50e+00 1.60e-01 3.75e+01 dihedral pdb=" C ARG B 183 " pdb=" N ARG B 183 " pdb=" CA ARG B 183 " pdb=" CB ARG B 183 " ideal model delta harmonic sigma weight residual -122.60 -134.68 12.08 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 6621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.388: 1746 1.388 - 2.776: 0 2.776 - 4.164: 0 4.164 - 5.552: 2 5.552 - 6.940: 2 Chirality restraints: 1750 Sorted by residual: chirality pdb=" N4 88T C 200 " pdb=" C11 88T C 200 " pdb=" C12 88T C 200 " pdb=" C22 88T C 200 " both_signs ideal model delta sigma weight residual False 4.34 -2.60 6.94 2.00e-01 2.50e+01 1.20e+03 chirality pdb=" N4 88T D 200 " pdb=" C11 88T D 200 " pdb=" C12 88T D 200 " pdb=" C22 88T D 200 " both_signs ideal model delta sigma weight residual False 4.34 -2.60 6.94 2.00e-01 2.50e+01 1.20e+03 chirality pdb=" N7 88T D 200 " pdb=" C19 88T D 200 " pdb=" C20 88T D 200 " pdb=" C23 88T D 200 " both_signs ideal model delta sigma weight residual False 2.45 -2.48 4.94 2.00e-01 2.50e+01 6.09e+02 ... (remaining 1747 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 281 " 0.024 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C ALA A 281 " -0.080 2.00e-02 2.50e+03 pdb=" O ALA A 281 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY A 282 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 601 " -0.048 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ANP A 601 " 0.021 2.00e-02 2.50e+03 pdb=" C4 ANP A 601 " 0.012 2.00e-02 2.50e+03 pdb=" C5 ANP A 601 " 0.015 2.00e-02 2.50e+03 pdb=" C6 ANP A 601 " 0.010 2.00e-02 2.50e+03 pdb=" C8 ANP A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N1 ANP A 601 " -0.011 2.00e-02 2.50e+03 pdb=" N3 ANP A 601 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ANP A 601 " -0.048 2.00e-02 2.50e+03 pdb=" N7 ANP A 601 " 0.027 2.00e-02 2.50e+03 pdb=" N9 ANP A 601 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP B 601 " 0.047 2.00e-02 2.50e+03 2.38e-02 1.56e+01 pdb=" C2 ANP B 601 " -0.019 2.00e-02 2.50e+03 pdb=" C4 ANP B 601 " -0.012 2.00e-02 2.50e+03 pdb=" C5 ANP B 601 " -0.014 2.00e-02 2.50e+03 pdb=" C6 ANP B 601 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ANP B 601 " -0.014 2.00e-02 2.50e+03 pdb=" N1 ANP B 601 " 0.010 2.00e-02 2.50e+03 pdb=" N3 ANP B 601 " -0.008 2.00e-02 2.50e+03 pdb=" N6 ANP B 601 " 0.047 2.00e-02 2.50e+03 pdb=" N7 ANP B 601 " -0.025 2.00e-02 2.50e+03 pdb=" N9 ANP B 601 " -0.001 2.00e-02 2.50e+03 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 86 2.60 - 3.17: 9699 3.17 - 3.75: 16791 3.75 - 4.32: 24408 4.32 - 4.90: 40298 Nonbonded interactions: 91282 Sorted by model distance: nonbonded pdb=" O2B ANP A 601 " pdb="MG MG A 602 " model vdw 2.022 2.170 nonbonded pdb="MG MG A 602 " pdb=" O HOH A 701 " model vdw 2.028 2.170 nonbonded pdb="MG MG A 602 " pdb=" O HOH A 702 " model vdw 2.031 2.170 nonbonded pdb=" O2G ANP B 601 " pdb="MG MG B 602 " model vdw 2.049 2.170 nonbonded pdb=" OG SER B 383 " pdb="MG MG B 602 " model vdw 2.052 2.170 ... (remaining 91277 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.09 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.890 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.870 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.041 2.793 11012 Z= 2.258 Angle : 1.534 74.772 14896 Z= 0.732 Chirality : 0.296 6.940 1750 Planarity : 0.007 0.117 1868 Dihedral : 15.877 178.430 4062 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.86 % 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: 0.17 (0.22), residues: 1370 helix: 1.03 (0.19), residues: 752 sheet: 0.08 (0.42), residues: 156 loop : -1.36 (0.26), residues: 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 1.364 Fit side-chains outliers start: 37 outliers final: 8 residues processed: 283 average time/residue: 1.5340 time to fit residues: 461.8848 Evaluate side-chains 191 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.7774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 307 GLN A 579 GLN B 579 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11012 Z= 0.197 Angle : 0.620 8.769 14896 Z= 0.302 Chirality : 0.043 0.283 1750 Planarity : 0.004 0.038 1868 Dihedral : 12.686 165.433 1564 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 5.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.23), residues: 1370 helix: 1.87 (0.19), residues: 764 sheet: -0.06 (0.40), residues: 174 loop : -1.02 (0.30), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 1.293 Fit side-chains outliers start: 61 outliers final: 24 residues processed: 233 average time/residue: 1.2655 time to fit residues: 317.7240 Evaluate side-chains 193 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.7181 time to fit residues: 7.4233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 0.0980 chunk 122 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 303 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS B 487 GLN B 576 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11012 Z= 0.284 Angle : 0.586 6.734 14896 Z= 0.299 Chirality : 0.043 0.165 1750 Planarity : 0.004 0.030 1868 Dihedral : 13.306 170.565 1564 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 5.85 % 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: 1.11 (0.23), residues: 1370 helix: 1.85 (0.18), residues: 762 sheet: -0.08 (0.40), residues: 174 loop : -0.91 (0.29), residues: 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 174 time to evaluate : 1.289 Fit side-chains outliers start: 68 outliers final: 29 residues processed: 219 average time/residue: 1.3161 time to fit residues: 309.5446 Evaluate side-chains 197 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.6715 time to fit residues: 7.1056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 303 ASN B 202 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 11012 Z= 0.377 Angle : 0.636 7.304 14896 Z= 0.322 Chirality : 0.045 0.177 1750 Planarity : 0.005 0.034 1868 Dihedral : 13.466 161.055 1564 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 6.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1370 helix: 1.62 (0.18), residues: 758 sheet: -0.14 (0.40), residues: 174 loop : -0.94 (0.29), residues: 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 170 time to evaluate : 1.396 Fit side-chains outliers start: 72 outliers final: 40 residues processed: 213 average time/residue: 1.3795 time to fit residues: 315.5058 Evaluate side-chains 209 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 10 average time/residue: 0.7193 time to fit residues: 9.9393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN C 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11012 Z= 0.207 Angle : 0.533 6.577 14896 Z= 0.272 Chirality : 0.041 0.167 1750 Planarity : 0.004 0.036 1868 Dihedral : 13.295 156.742 1564 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 4.65 % 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: 1.18 (0.23), residues: 1370 helix: 1.95 (0.19), residues: 762 sheet: -0.06 (0.39), residues: 176 loop : -0.95 (0.29), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 1.265 Fit side-chains outliers start: 54 outliers final: 30 residues processed: 206 average time/residue: 1.2679 time to fit residues: 282.1124 Evaluate side-chains 191 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 0.6720 time to fit residues: 4.1612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 303 ASN B 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 11012 Z= 0.332 Angle : 0.598 6.889 14896 Z= 0.305 Chirality : 0.044 0.174 1750 Planarity : 0.004 0.036 1868 Dihedral : 13.299 151.336 1564 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 5.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.23), residues: 1370 helix: 1.69 (0.18), residues: 764 sheet: -0.07 (0.39), residues: 176 loop : -0.94 (0.29), residues: 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 171 time to evaluate : 1.266 Fit side-chains outliers start: 61 outliers final: 38 residues processed: 209 average time/residue: 1.3165 time to fit residues: 296.0650 Evaluate side-chains 207 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 11 average time/residue: 0.7713 time to fit residues: 11.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11012 Z= 0.186 Angle : 0.514 6.793 14896 Z= 0.263 Chirality : 0.040 0.165 1750 Planarity : 0.004 0.036 1868 Dihedral : 13.149 144.355 1564 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 3.27 % 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: 1.29 (0.23), residues: 1370 helix: 2.04 (0.19), residues: 762 sheet: -0.02 (0.39), residues: 176 loop : -0.91 (0.29), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 1.299 Fit side-chains outliers start: 38 outliers final: 25 residues processed: 204 average time/residue: 1.3398 time to fit residues: 294.3236 Evaluate side-chains 190 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 1.0749 time to fit residues: 4.1472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 11012 Z= 0.277 Angle : 0.566 8.872 14896 Z= 0.288 Chirality : 0.042 0.172 1750 Planarity : 0.004 0.036 1868 Dihedral : 13.183 141.544 1564 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.84 % 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: 1.14 (0.23), residues: 1370 helix: 1.85 (0.19), residues: 762 sheet: 0.13 (0.40), residues: 186 loop : -0.98 (0.28), residues: 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.168 Fit side-chains outliers start: 33 outliers final: 25 residues processed: 191 average time/residue: 1.3208 time to fit residues: 271.4170 Evaluate side-chains 190 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.6073 time to fit residues: 3.2328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 303 ASN B 202 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11012 Z= 0.191 Angle : 0.520 9.072 14896 Z= 0.265 Chirality : 0.040 0.160 1750 Planarity : 0.004 0.036 1868 Dihedral : 13.153 141.410 1564 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.84 % 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: 1.35 (0.23), residues: 1370 helix: 2.05 (0.19), residues: 762 sheet: 0.15 (0.40), residues: 186 loop : -0.92 (0.29), residues: 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.437 Fit side-chains outliers start: 33 outliers final: 25 residues processed: 190 average time/residue: 1.3843 time to fit residues: 283.7392 Evaluate side-chains 187 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.9900 time to fit residues: 5.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 0.0370 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 11012 Z= 0.151 Angle : 0.505 9.872 14896 Z= 0.255 Chirality : 0.040 0.159 1750 Planarity : 0.004 0.037 1868 Dihedral : 13.128 144.725 1564 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1370 helix: 2.27 (0.19), residues: 762 sheet: 0.18 (0.39), residues: 186 loop : -0.86 (0.29), residues: 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.983 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 195 average time/residue: 1.2563 time to fit residues: 264.8441 Evaluate side-chains 184 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125030 restraints weight = 6370.173| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.40 r_work: 0.3279 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11012 Z= 0.177 Angle : 0.521 10.047 14896 Z= 0.265 Chirality : 0.040 0.158 1750 Planarity : 0.004 0.039 1868 Dihedral : 13.155 145.725 1564 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.15 % 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: 1.59 (0.23), residues: 1370 helix: 2.25 (0.19), residues: 762 sheet: 0.18 (0.39), residues: 186 loop : -0.78 (0.29), residues: 422 =============================================================================== Job complete usr+sys time: 5007.07 seconds wall clock time: 89 minutes 13.51 seconds (5353.51 seconds total)