Starting phenix.real_space_refine on Thu Feb 15 02:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_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_13406/02_2024/7ph4_13406_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph4_13406/02_2024/7ph4_13406_updated.pdb" } resolution = 2.8 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= 0.002 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.76, per 1000 atoms: 0.53 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: 23.01 Conformation dependent library (CDL) restraints added in 1.9 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: 3.19 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: 2.80 Time building geometry restraints manager: 4.55 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 - 35.78: 6576 35.78 - 71.56: 156 71.56 - 107.33: 48 107.33 - 143.11: 16 143.11 - 178.89: 8 Dihedral angle restraints: 6804 sinusoidal: 2836 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 6801 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: 1.630 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: 7.070 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.520 Find NCS groups from input model: 0.510 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.860 ------------------------------------------------------------------------------- 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 : 19.989 178.887 4242 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 % Allowed : 8.43 % Favored : 88.38 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 17 HIS 0.005 0.001 HIS B 568 PHE 0.032 0.003 PHE B 462 TYR 0.028 0.002 TYR C 59 ARG 0.010 0.001 ARG A 15 *********************** 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 : 1.175 Fit side-chains REVERT: A 14 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7440 (mtm-85) REVERT: A 180 ILE cc_start: 0.8059 (pp) cc_final: 0.7788 (pt) REVERT: A 208 GLU cc_start: 0.7671 (tp30) cc_final: 0.7429 (tm-30) REVERT: A 244 MET cc_start: 0.8844 (tpt) cc_final: 0.8553 (tpt) REVERT: A 295 MET cc_start: 0.7986 (mtm) cc_final: 0.7650 (mtm) REVERT: A 334 VAL cc_start: 0.8792 (m) cc_final: 0.8565 (t) REVERT: B 208 GLU cc_start: 0.7630 (tp30) cc_final: 0.7414 (tm-30) REVERT: B 225 VAL cc_start: 0.8574 (t) cc_final: 0.8221 (m) REVERT: C 94 TYR cc_start: 0.8456 (m-80) cc_final: 0.8210 (m-80) REVERT: D 56 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7095 (ttm110) REVERT: D 81 GLN cc_start: 0.8221 (tp40) cc_final: 0.7987 (tp40) outliers start: 37 outliers final: 8 residues processed: 283 average time/residue: 1.4487 time to fit residues: 435.1987 Evaluate side-chains 192 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain D residue 78 VAL 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: 0.7980 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11012 Z= 0.183 Angle : 0.621 8.350 14896 Z= 0.299 Chirality : 0.043 0.296 1750 Planarity : 0.004 0.033 1868 Dihedral : 18.943 166.753 1752 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.65 % Allowed : 17.30 % Favored : 78.06 % 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: 1.15 (0.23), residues: 1370 helix: 1.95 (0.19), residues: 764 sheet: -0.06 (0.40), residues: 174 loop : -1.04 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 17 HIS 0.006 0.001 HIS A 568 PHE 0.015 0.001 PHE B 462 TYR 0.013 0.001 TYR D 94 ARG 0.004 0.000 ARG C 56 *********************** 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 243 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 189 time to evaluate : 1.123 Fit side-chains REVERT: A 202 GLN cc_start: 0.8001 (mt0) cc_final: 0.7720 (mt0) REVERT: A 547 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: A 574 GLN cc_start: 0.7845 (mm110) cc_final: 0.7391 (mt0) REVERT: B 87 TYR cc_start: 0.8555 (t80) cc_final: 0.8321 (t80) REVERT: B 202 GLN cc_start: 0.8003 (mt0) cc_final: 0.7736 (mt0) REVERT: B 455 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7820 (ttt-90) REVERT: B 487 GLN cc_start: 0.8318 (tt0) cc_final: 0.8110 (tt0) REVERT: B 547 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: C 56 ARG cc_start: 0.7269 (mmm160) cc_final: 0.6654 (ttp-110) REVERT: D 81 GLN cc_start: 0.8083 (tp40) cc_final: 0.7818 (tp-100) REVERT: D 98 GLU cc_start: 0.8233 (pt0) cc_final: 0.7893 (pt0) outliers start: 54 outliers final: 21 residues processed: 225 average time/residue: 1.1994 time to fit residues: 289.9316 Evaluate side-chains 189 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 7 SER 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: 0.6980 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 0.2980 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.0010 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11012 Z= 0.208 Angle : 0.554 7.571 14896 Z= 0.278 Chirality : 0.042 0.275 1750 Planarity : 0.004 0.031 1868 Dihedral : 18.668 167.085 1748 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.08 % Allowed : 18.67 % Favored : 76.25 % 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: 1.40 (0.23), residues: 1370 helix: 2.16 (0.19), residues: 762 sheet: 0.03 (0.40), residues: 174 loop : -0.94 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.006 0.001 HIS A 568 PHE 0.020 0.001 PHE A 462 TYR 0.013 0.001 TYR D 94 ARG 0.003 0.000 ARG A 530 *********************** 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 241 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 182 time to evaluate : 1.382 Fit side-chains REVERT: A 6 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7362 (t70) REVERT: A 172 ILE cc_start: 0.8392 (mm) cc_final: 0.7897 (pt) REVERT: A 202 GLN cc_start: 0.7996 (mt0) cc_final: 0.7712 (mt0) REVERT: A 547 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: B 14 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7211 (mtt-85) REVERT: B 87 TYR cc_start: 0.8574 (t80) cc_final: 0.8337 (t80) REVERT: B 172 ILE cc_start: 0.8311 (mm) cc_final: 0.7739 (pt) REVERT: B 202 GLN cc_start: 0.8024 (mt0) cc_final: 0.7736 (mt0) REVERT: B 452 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: B 455 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7772 (ttt-90) REVERT: B 520 GLN cc_start: 0.7991 (tp40) cc_final: 0.7669 (tm-30) REVERT: B 524 ASP cc_start: 0.7068 (m-30) cc_final: 0.6859 (m-30) REVERT: B 547 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: C 56 ARG cc_start: 0.7460 (mmm160) cc_final: 0.6798 (ttp-110) REVERT: D 98 GLU cc_start: 0.8324 (pt0) cc_final: 0.7920 (pt0) outliers start: 59 outliers final: 23 residues processed: 221 average time/residue: 1.3375 time to fit residues: 316.5221 Evaluate side-chains 200 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 124 optimal weight: 0.0870 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 487 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: 0.8103 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11012 Z= 0.160 Angle : 0.510 7.595 14896 Z= 0.255 Chirality : 0.040 0.182 1750 Planarity : 0.004 0.034 1868 Dihedral : 18.619 172.598 1748 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.30 % Allowed : 19.19 % Favored : 76.51 % 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: 1.66 (0.23), residues: 1370 helix: 2.40 (0.19), residues: 762 sheet: 0.10 (0.40), residues: 164 loop : -0.85 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 17 HIS 0.005 0.001 HIS B 568 PHE 0.016 0.001 PHE B 308 TYR 0.012 0.001 TYR D 94 ARG 0.003 0.000 ARG A 530 *********************** 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 234 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 184 time to evaluate : 1.241 Fit side-chains REVERT: A 6 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7287 (t70) REVERT: A 101 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: A 172 ILE cc_start: 0.8259 (mm) cc_final: 0.7961 (pt) REVERT: A 202 GLN cc_start: 0.7980 (mt0) cc_final: 0.7725 (mt0) REVERT: A 295 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7390 (ttm) REVERT: A 547 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: A 574 GLN cc_start: 0.7867 (mm110) cc_final: 0.7401 (mt0) REVERT: B 87 TYR cc_start: 0.8445 (t80) cc_final: 0.8214 (t80) REVERT: B 202 GLN cc_start: 0.7968 (mt0) cc_final: 0.7694 (mt0) REVERT: B 455 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7846 (ttt-90) REVERT: B 547 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: C 56 ARG cc_start: 0.7433 (mmm160) cc_final: 0.6850 (ttp-110) REVERT: D 4 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7980 (pp) REVERT: D 98 GLU cc_start: 0.8247 (pt0) cc_final: 0.7836 (pt0) outliers start: 50 outliers final: 25 residues processed: 215 average time/residue: 1.1570 time to fit residues: 266.6382 Evaluate side-chains 207 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3029 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= 0.168 Angle : 0.504 6.370 14896 Z= 0.255 Chirality : 0.040 0.158 1750 Planarity : 0.004 0.037 1868 Dihedral : 18.595 173.347 1748 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.65 % Allowed : 19.54 % Favored : 75.82 % 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: 1.72 (0.23), residues: 1370 helix: 2.47 (0.19), residues: 762 sheet: 0.09 (0.39), residues: 174 loop : -0.86 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.005 0.001 HIS B 568 PHE 0.016 0.001 PHE B 308 TYR 0.011 0.001 TYR D 94 ARG 0.003 0.000 ARG A 530 *********************** 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 232 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 1.332 Fit side-chains REVERT: A 75 MET cc_start: 0.7489 (mmm) cc_final: 0.7238 (mmt) REVERT: A 101 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8088 (mtt-85) REVERT: A 202 GLN cc_start: 0.7995 (mt0) cc_final: 0.7715 (mt0) REVERT: A 547 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: A 574 GLN cc_start: 0.7872 (mm110) cc_final: 0.7374 (mt0) REVERT: B 87 TYR cc_start: 0.8491 (t80) cc_final: 0.8249 (t80) REVERT: B 101 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8066 (mtt-85) REVERT: B 202 GLN cc_start: 0.7960 (mt0) cc_final: 0.7695 (mt0) REVERT: B 547 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: C 56 ARG cc_start: 0.7498 (mmm160) cc_final: 0.6925 (ttp-110) REVERT: D 4 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7974 (pp) REVERT: D 98 GLU cc_start: 0.8215 (pt0) cc_final: 0.7809 (pt0) outliers start: 54 outliers final: 28 residues processed: 210 average time/residue: 1.2547 time to fit residues: 283.0634 Evaluate side-chains 200 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 37 ASN ** 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: 0.8143 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11012 Z= 0.220 Angle : 0.542 7.704 14896 Z= 0.273 Chirality : 0.041 0.158 1750 Planarity : 0.004 0.038 1868 Dihedral : 18.773 174.652 1748 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.82 % Allowed : 19.88 % Favored : 75.30 % 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: 1.55 (0.23), residues: 1370 helix: 2.27 (0.18), residues: 762 sheet: 0.08 (0.40), residues: 174 loop : -0.85 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 17 HIS 0.006 0.001 HIS A 568 PHE 0.021 0.002 PHE A 462 TYR 0.011 0.001 TYR D 94 ARG 0.002 0.000 ARG B 148 *********************** 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 220 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 164 time to evaluate : 1.203 Fit side-chains REVERT: A 75 MET cc_start: 0.7571 (mmm) cc_final: 0.7315 (mmt) REVERT: A 101 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8097 (mtt-85) REVERT: A 202 GLN cc_start: 0.8002 (mt0) cc_final: 0.7715 (mt0) REVERT: A 243 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7599 (mtmm) REVERT: A 517 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7294 (mtp180) REVERT: A 547 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: B 87 TYR cc_start: 0.8528 (t80) cc_final: 0.8271 (t80) REVERT: B 101 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8068 (mtt-85) REVERT: B 167 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6162 (mt) REVERT: B 202 GLN cc_start: 0.8016 (mt0) cc_final: 0.7708 (mt0) REVERT: B 517 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7287 (mtp180) REVERT: B 520 GLN cc_start: 0.7856 (tp40) cc_final: 0.7587 (tm-30) REVERT: B 547 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: C 56 ARG cc_start: 0.7480 (mmm160) cc_final: 0.6876 (ttp-110) REVERT: D 4 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7932 (pp) REVERT: D 98 GLU cc_start: 0.8272 (pt0) cc_final: 0.7897 (pt0) outliers start: 56 outliers final: 23 residues processed: 201 average time/residue: 1.1040 time to fit residues: 238.2195 Evaluate side-chains 189 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3044 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= 0.216 Angle : 0.535 8.308 14896 Z= 0.270 Chirality : 0.041 0.159 1750 Planarity : 0.004 0.037 1868 Dihedral : 18.797 175.302 1748 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.79 % Allowed : 21.17 % Favored : 75.04 % 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: 1.53 (0.23), residues: 1370 helix: 2.25 (0.18), residues: 762 sheet: 0.03 (0.39), residues: 174 loop : -0.82 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 HIS 0.006 0.001 HIS B 568 PHE 0.020 0.002 PHE B 462 TYR 0.011 0.001 TYR D 94 ARG 0.002 0.000 ARG A 530 *********************** 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 213 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.152 Fit side-chains REVERT: A 75 MET cc_start: 0.7585 (mmm) cc_final: 0.7335 (mmt) REVERT: A 101 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8106 (mtt-85) REVERT: A 202 GLN cc_start: 0.8008 (mt0) cc_final: 0.7721 (mt0) REVERT: A 517 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7290 (mtp180) REVERT: A 547 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: A 574 GLN cc_start: 0.7883 (mm110) cc_final: 0.7381 (mt0) REVERT: B 87 TYR cc_start: 0.8564 (t80) cc_final: 0.8334 (t80) REVERT: B 101 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8066 (mtt-85) REVERT: B 202 GLN cc_start: 0.8020 (mt0) cc_final: 0.7678 (mt0) REVERT: B 517 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: B 547 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: C 56 ARG cc_start: 0.7445 (mmm160) cc_final: 0.6948 (ttp-110) REVERT: D 4 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7951 (pp) REVERT: D 81 GLN cc_start: 0.8187 (tp40) cc_final: 0.7914 (tp-100) REVERT: D 98 GLU cc_start: 0.8273 (pt0) cc_final: 0.7904 (pt0) outliers start: 44 outliers final: 24 residues processed: 201 average time/residue: 1.1810 time to fit residues: 255.1322 Evaluate side-chains 196 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11012 Z= 0.372 Angle : 0.633 10.252 14896 Z= 0.318 Chirality : 0.045 0.166 1750 Planarity : 0.004 0.036 1868 Dihedral : 19.227 176.011 1748 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.04 % Allowed : 21.08 % Favored : 74.87 % 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: 1.13 (0.23), residues: 1370 helix: 1.81 (0.18), residues: 762 sheet: 0.11 (0.40), residues: 184 loop : -0.88 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 17 HIS 0.007 0.001 HIS A 568 PHE 0.030 0.002 PHE B 462 TYR 0.010 0.002 TYR D 94 ARG 0.003 0.000 ARG B 148 *********************** 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 220 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 173 time to evaluate : 1.124 Fit side-chains REVERT: A 75 MET cc_start: 0.7667 (mmm) cc_final: 0.7381 (mmt) REVERT: A 101 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8126 (mtt-85) REVERT: A 172 ILE cc_start: 0.8328 (mm) cc_final: 0.7868 (pt) REVERT: A 202 GLN cc_start: 0.8104 (mt0) cc_final: 0.7782 (mt0) REVERT: A 517 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7344 (mtp180) REVERT: A 547 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: B 86 SER cc_start: 0.8457 (m) cc_final: 0.8248 (m) REVERT: B 101 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8067 (mtt-85) REVERT: B 172 ILE cc_start: 0.8485 (mm) cc_final: 0.7820 (pt) REVERT: B 517 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7351 (mtp180) REVERT: B 547 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: C 56 ARG cc_start: 0.7510 (mmm160) cc_final: 0.6804 (ttp-110) outliers start: 47 outliers final: 25 residues processed: 204 average time/residue: 1.1404 time to fit residues: 249.3016 Evaluate side-chains 195 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.2980 chunk 125 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3386 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: