Starting phenix.real_space_refine on Sat Feb 17 23:06:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcq_12142/02_2024/7bcq_12142_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6453 2.51 5 N 1626 2.21 5 O 1734 1.98 5 H 10299 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ARG 376": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B ARG 376": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "B ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C ARG 376": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C ASP 487": "OD1" <-> "OD2" Residue "C ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 6697 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "B" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 6697 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "C" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 6697 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TG2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TG2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TG2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.44, per 1000 atoms: 0.47 Number of scatterers: 20160 At special positions: 0 Unit cell: (106.26, 105.248, 77.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1734 8.00 N 1626 7.00 C 6453 6.00 H 10299 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.90 Conformation dependent library (CDL) restraints added in 2.3 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 3 sheets defined 74.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 53 through 75 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 83 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.704A pdb=" N ALA A 117 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 250 through 290 removed outlier: 4.480A pdb=" N LEU A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 260 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.533A pdb=" N PHE A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 removed outlier: 6.604A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.647A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 372 through 384 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 412 through 427 removed outlier: 4.336A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.643A pdb=" N VAL A 446 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.519A pdb=" N ILE A 456 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.728A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 53 through 75 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 83 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.703A pdb=" N ALA B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 153 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 231 through 247 Processing helix chain 'B' and resid 250 through 290 removed outlier: 4.479A pdb=" N LEU B 254 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 260 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.534A pdb=" N PHE B 283 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 318 removed outlier: 6.603A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.647A pdb=" N ILE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 372 through 384 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 388 through 403 Processing helix chain 'B' and resid 412 through 427 removed outlier: 4.336A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 removed outlier: 3.643A pdb=" N VAL B 446 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.518A pdb=" N ILE B 456 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 487 removed outlier: 4.728A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 53 through 75 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 83 through 101 Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.704A pdb=" N ALA C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 231 through 247 Processing helix chain 'C' and resid 250 through 290 removed outlier: 4.479A pdb=" N LEU C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 260 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.533A pdb=" N PHE C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 6.604A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 329 Processing helix chain 'C' and resid 333 through 350 removed outlier: 3.648A pdb=" N ILE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 357 through 366 Processing helix chain 'C' and resid 372 through 384 Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 388 through 403 Processing helix chain 'C' and resid 412 through 427 removed outlier: 4.337A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 446 removed outlier: 3.644A pdb=" N VAL C 446 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.517A pdb=" N ILE C 456 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 458 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.728A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 202 through 209 removed outlier: 3.705A pdb=" N SER A 205 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 202 through 209 removed outlier: 3.704A pdb=" N SER B 205 " --> pdb=" O GLN B 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 202 through 209 removed outlier: 3.704A pdb=" N SER C 205 " --> pdb=" O GLN C 224 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1647 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: 7.11 Time building geometry restraints manager: 17.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10278 1.03 - 1.23: 32 1.23 - 1.42: 3970 1.42 - 1.62: 5988 1.62 - 1.81: 75 Bond restraints: 20343 Sorted by residual: bond pdb=" C01 TG2 C 601 " pdb=" C02 TG2 C 601 " ideal model delta sigma weight residual 1.320 1.478 -0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C01 TG2 B 601 " pdb=" C02 TG2 B 601 " ideal model delta sigma weight residual 1.320 1.478 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" C01 TG2 A 601 " pdb=" C02 TG2 A 601 " ideal model delta sigma weight residual 1.320 1.478 -0.158 2.00e-02 2.50e+03 6.21e+01 bond pdb=" C05 TG2 C 601 " pdb=" N04 TG2 C 601 " ideal model delta sigma weight residual 1.310 1.464 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C05 TG2 B 601 " pdb=" N04 TG2 B 601 " ideal model delta sigma weight residual 1.310 1.463 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 20338 not shown) Histogram of bond angle deviations from ideal: 82.25 - 92.65: 36 92.65 - 103.05: 66 103.05 - 113.45: 24991 113.45 - 123.85: 10415 123.85 - 134.25: 1473 Bond angle restraints: 36981 Sorted by residual: angle pdb=" CD1 LEU C 269 " pdb=" CG LEU C 269 " pdb=" HG LEU C 269 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" CD1 LEU B 269 " pdb=" CG LEU B 269 " pdb=" HG LEU B 269 " ideal model delta sigma weight residual 108.00 82.59 25.41 3.00e+00 1.11e-01 7.17e+01 angle pdb=" CD1 LEU A 269 " pdb=" CG LEU A 269 " pdb=" HG LEU A 269 " ideal model delta sigma weight residual 108.00 82.60 25.40 3.00e+00 1.11e-01 7.17e+01 angle pdb=" CD2 LEU B 149 " pdb=" CG LEU B 149 " pdb=" HG LEU B 149 " ideal model delta sigma weight residual 108.00 83.02 24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" CD2 LEU A 149 " pdb=" CG LEU A 149 " pdb=" HG LEU A 149 " ideal model delta sigma weight residual 108.00 83.03 24.97 3.00e+00 1.11e-01 6.93e+01 ... (remaining 36976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 8189 17.39 - 34.79: 842 34.79 - 52.18: 241 52.18 - 69.57: 152 69.57 - 86.96: 32 Dihedral angle restraints: 9456 sinusoidal: 5178 harmonic: 4278 Sorted by residual: dihedral pdb=" CA ASN C 190 " pdb=" C ASN C 190 " pdb=" N ILE C 191 " pdb=" CA ILE C 191 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN B 190 " pdb=" C ASN B 190 " pdb=" N ILE B 191 " pdb=" CA ILE B 191 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN A 190 " pdb=" C ASN A 190 " pdb=" N ILE A 191 " pdb=" CA ILE A 191 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 9453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1692 0.349 - 0.697: 0 0.697 - 1.046: 0 1.046 - 1.394: 0 1.394 - 1.743: 12 Chirality restraints: 1704 Sorted by residual: chirality pdb=" CG LEU B 149 " pdb=" CB LEU B 149 " pdb=" CD1 LEU B 149 " pdb=" CD2 LEU B 149 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.59e+01 chirality pdb=" CG LEU A 149 " pdb=" CB LEU A 149 " pdb=" CD1 LEU A 149 " pdb=" CD2 LEU A 149 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.59e+01 chirality pdb=" CG LEU C 149 " pdb=" CB LEU C 149 " pdb=" CD1 LEU C 149 " pdb=" CD2 LEU C 149 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.59e+01 ... (remaining 1701 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 335 " 0.144 9.50e-02 1.11e+02 5.51e-02 1.90e+01 pdb=" NE ARG C 335 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG C 335 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG C 335 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 335 " 0.031 2.00e-02 2.50e+03 pdb="HH11 ARG C 335 " 0.019 2.00e-02 2.50e+03 pdb="HH12 ARG C 335 " -0.028 2.00e-02 2.50e+03 pdb="HH21 ARG C 335 " 0.006 2.00e-02 2.50e+03 pdb="HH22 ARG C 335 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 335 " 0.144 9.50e-02 1.11e+02 5.52e-02 1.88e+01 pdb=" NE ARG A 335 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 335 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 335 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 335 " 0.030 2.00e-02 2.50e+03 pdb="HH11 ARG A 335 " 0.019 2.00e-02 2.50e+03 pdb="HH12 ARG A 335 " -0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 335 " 0.006 2.00e-02 2.50e+03 pdb="HH22 ARG A 335 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " -0.143 9.50e-02 1.11e+02 5.48e-02 1.86e+01 pdb=" NE ARG B 335 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG B 335 " -0.019 2.00e-02 2.50e+03 pdb="HH12 ARG B 335 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG B 335 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG B 335 " 0.025 2.00e-02 2.50e+03 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 3626 2.29 - 2.87: 46580 2.87 - 3.44: 54490 3.44 - 4.02: 71632 4.02 - 4.60: 110564 Nonbonded interactions: 286892 Sorted by model distance: nonbonded pdb="HH11 ARG B 189 " pdb=" OE1 GLU C 94 " model vdw 1.711 1.850 nonbonded pdb="HD21 ASN A 195 " pdb=" O ALA B 200 " model vdw 1.713 1.850 nonbonded pdb=" OE2 GLU A 227 " pdb="HH12 ARG C 202 " model vdw 1.716 1.850 nonbonded pdb=" O ARG A 189 " pdb="HH21 ARG B 98 " model vdw 1.725 1.850 nonbonded pdb=" O ALA A 200 " pdb="HD21 ASN C 195 " model vdw 1.734 1.850 ... (remaining 286887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.300 Extract box with map and model: 2.820 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 66.860 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.012 0.158 10044 Z= 0.805 Angle : 1.052 11.942 13692 Z= 0.518 Chirality : 0.154 1.743 1704 Planarity : 0.007 0.092 1707 Dihedral : 13.766 86.732 3495 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.68 (0.22), residues: 1320 helix: 0.21 (0.15), residues: 975 sheet: -3.09 (0.47), residues: 42 loop : -1.95 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 338 HIS 0.007 0.002 HIS A 373 PHE 0.045 0.003 PHE A 393 TYR 0.018 0.003 TYR C 325 ARG 0.033 0.002 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 ILE cc_start: 0.7452 (mt) cc_final: 0.7069 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3929 time to fit residues: 52.3975 Evaluate side-chains 79 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10044 Z= 0.206 Angle : 0.692 11.369 13692 Z= 0.324 Chirality : 0.148 1.756 1704 Planarity : 0.005 0.045 1707 Dihedral : 5.251 45.099 1425 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % 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: 0.02 (0.23), residues: 1320 helix: 0.72 (0.17), residues: 969 sheet: -2.73 (0.53), residues: 42 loop : -1.68 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 461 HIS 0.003 0.001 HIS B 313 PHE 0.020 0.001 PHE A 393 TYR 0.008 0.001 TYR C 204 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 ILE cc_start: 0.7759 (mt) cc_final: 0.7323 (tp) REVERT: B 417 ILE cc_start: 0.7426 (mt) cc_final: 0.7106 (tp) REVERT: C 274 MET cc_start: 0.6879 (ttp) cc_final: 0.6617 (ttp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.5553 time to fit residues: 65.5408 Evaluate side-chains 81 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10044 Z= 0.281 Angle : 0.698 10.823 13692 Z= 0.326 Chirality : 0.147 1.718 1704 Planarity : 0.005 0.042 1707 Dihedral : 4.712 40.487 1425 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.39 % Allowed : 5.44 % Favored : 94.17 % 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: 0.15 (0.24), residues: 1320 helix: 0.76 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.023 0.002 PHE A 393 TYR 0.010 0.001 TYR C 325 ARG 0.005 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.7673 (tpp) cc_final: 0.7315 (tpp) REVERT: A 417 ILE cc_start: 0.7754 (mt) cc_final: 0.7209 (tp) REVERT: B 417 ILE cc_start: 0.7477 (mt) cc_final: 0.7107 (tp) REVERT: C 417 ILE cc_start: 0.7551 (mt) cc_final: 0.6909 (tp) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.4239 time to fit residues: 71.6269 Evaluate side-chains 99 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10044 Z= 0.235 Angle : 0.666 10.603 13692 Z= 0.305 Chirality : 0.147 1.711 1704 Planarity : 0.004 0.039 1707 Dihedral : 4.610 38.598 1425 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.39 % Allowed : 6.41 % Favored : 93.20 % 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: 0.21 (0.24), residues: 1320 helix: 0.84 (0.17), residues: 975 sheet: -2.73 (0.61), residues: 42 loop : -1.52 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 PHE 0.015 0.001 PHE C 393 TYR 0.008 0.001 TYR C 204 ARG 0.004 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.7807 (tpp) cc_final: 0.7485 (tpp) REVERT: A 417 ILE cc_start: 0.7745 (mt) cc_final: 0.7188 (tp) REVERT: B 417 ILE cc_start: 0.7514 (mt) cc_final: 0.7130 (tp) REVERT: C 224 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: C 417 ILE cc_start: 0.7661 (mt) cc_final: 0.7034 (tp) outliers start: 4 outliers final: 2 residues processed: 116 average time/residue: 0.4243 time to fit residues: 73.3906 Evaluate side-chains 111 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 224 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10044 Z= 0.409 Angle : 0.734 10.889 13692 Z= 0.351 Chirality : 0.148 1.723 1704 Planarity : 0.005 0.043 1707 Dihedral : 4.763 39.122 1425 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.68 % Allowed : 8.16 % Favored : 91.16 % 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: -0.19 (0.23), residues: 1320 helix: 0.51 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 275 HIS 0.002 0.001 HIS A 313 PHE 0.017 0.002 PHE C 393 TYR 0.012 0.002 TYR A 325 ARG 0.005 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7839 (mptt) cc_final: 0.7524 (mptt) REVERT: A 360 MET cc_start: 0.8013 (tpp) cc_final: 0.7641 (tpt) REVERT: A 417 ILE cc_start: 0.7809 (mt) cc_final: 0.7204 (tp) REVERT: A 473 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8276 (tm-30) outliers start: 7 outliers final: 6 residues processed: 136 average time/residue: 0.4281 time to fit residues: 87.3126 Evaluate side-chains 131 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10044 Z= 0.175 Angle : 0.648 10.738 13692 Z= 0.293 Chirality : 0.146 1.710 1704 Planarity : 0.004 0.039 1707 Dihedral : 4.429 35.575 1425 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.06 % 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: 0.22 (0.24), residues: 1320 helix: 0.83 (0.17), residues: 975 sheet: -2.94 (0.64), residues: 42 loop : -1.45 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 338 HIS 0.002 0.001 HIS B 313 PHE 0.011 0.001 PHE C 393 TYR 0.007 0.001 TYR A 204 ARG 0.002 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: A 360 MET cc_start: 0.8007 (tpp) cc_final: 0.7532 (tpt) REVERT: A 417 ILE cc_start: 0.7759 (mt) cc_final: 0.7176 (tp) REVERT: A 473 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 224 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: C 417 ILE cc_start: 0.7703 (mt) cc_final: 0.7098 (tp) outliers start: 6 outliers final: 2 residues processed: 121 average time/residue: 0.4308 time to fit residues: 77.5725 Evaluate side-chains 114 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10044 Z= 0.205 Angle : 0.653 10.727 13692 Z= 0.296 Chirality : 0.146 1.703 1704 Planarity : 0.004 0.039 1707 Dihedral : 4.383 35.437 1425 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.58 % Allowed : 8.65 % Favored : 90.77 % 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: 0.37 (0.24), residues: 1320 helix: 0.89 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 130 HIS 0.002 0.001 HIS C 313 PHE 0.011 0.001 PHE C 393 TYR 0.007 0.001 TYR A 334 ARG 0.003 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7783 (mptt) cc_final: 0.7434 (mptt) REVERT: A 360 MET cc_start: 0.8032 (tpp) cc_final: 0.7553 (tpp) REVERT: A 417 ILE cc_start: 0.7772 (mt) cc_final: 0.7198 (tp) REVERT: B 224 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: C 224 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: C 417 ILE cc_start: 0.7676 (mt) cc_final: 0.7088 (tp) outliers start: 6 outliers final: 3 residues processed: 117 average time/residue: 0.4333 time to fit residues: 74.8838 Evaluate side-chains 114 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10044 Z= 0.203 Angle : 0.653 10.712 13692 Z= 0.295 Chirality : 0.146 1.701 1704 Planarity : 0.004 0.040 1707 Dihedral : 4.332 34.561 1425 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.68 % Allowed : 8.75 % Favored : 90.57 % 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: 0.48 (0.24), residues: 1320 helix: 0.96 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.46 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 130 HIS 0.002 0.001 HIS C 313 PHE 0.009 0.001 PHE B 393 TYR 0.008 0.001 TYR A 334 ARG 0.005 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: A 288 LYS cc_start: 0.7803 (mptt) cc_final: 0.7443 (mptt) REVERT: A 360 MET cc_start: 0.8014 (tpp) cc_final: 0.7592 (tpp) REVERT: A 417 ILE cc_start: 0.7790 (mt) cc_final: 0.7202 (tp) REVERT: B 224 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: C 224 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: C 417 ILE cc_start: 0.7672 (mt) cc_final: 0.7103 (tp) outliers start: 7 outliers final: 3 residues processed: 117 average time/residue: 0.4510 time to fit residues: 78.3009 Evaluate side-chains 114 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10044 Z= 0.185 Angle : 0.648 10.679 13692 Z= 0.291 Chirality : 0.146 1.700 1704 Planarity : 0.004 0.051 1707 Dihedral : 4.255 33.461 1425 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.58 % Allowed : 9.14 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1320 helix: 1.01 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.41 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 338 HIS 0.002 0.001 HIS C 313 PHE 0.008 0.001 PHE B 393 TYR 0.007 0.001 TYR A 334 ARG 0.005 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: A 360 MET cc_start: 0.7996 (tpp) cc_final: 0.7608 (tpp) REVERT: A 417 ILE cc_start: 0.7778 (mt) cc_final: 0.7207 (tp) REVERT: B 224 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: C 224 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7375 (pt0) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.4333 time to fit residues: 71.6248 Evaluate side-chains 112 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10044 Z= 0.157 Angle : 0.637 10.603 13692 Z= 0.284 Chirality : 0.146 1.700 1704 Planarity : 0.004 0.049 1707 Dihedral : 4.088 31.087 1425 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.39 % Allowed : 9.43 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1320 helix: 1.20 (0.18), residues: 972 sheet: None (None), residues: 0 loop : -1.41 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 338 HIS 0.003 0.001 HIS C 313 PHE 0.008 0.001 PHE A 258 TYR 0.006 0.001 TYR B 334 ARG 0.005 0.000 ARG A 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: A 360 MET cc_start: 0.7904 (tpp) cc_final: 0.7560 (tpp) REVERT: A 417 ILE cc_start: 0.7729 (mt) cc_final: 0.7247 (tp) REVERT: B 417 ILE cc_start: 0.7543 (mt) cc_final: 0.7169 (tp) outliers start: 4 outliers final: 3 residues processed: 108 average time/residue: 0.4219 time to fit residues: 68.4250 Evaluate side-chains 108 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.0270 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.224712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.170367 restraints weight = 29891.082| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.25 r_work: 0.3601 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10044 Z= 0.151 Angle : 0.634 10.620 13692 Z= 0.280 Chirality : 0.146 1.700 1704 Planarity : 0.004 0.038 1707 Dihedral : 3.967 29.705 1425 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.58 % Allowed : 9.33 % Favored : 90.09 % 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: 0.92 (0.25), residues: 1320 helix: 1.30 (0.18), residues: 972 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 338 HIS 0.002 0.001 HIS B 313 PHE 0.007 0.001 PHE C 258 TYR 0.005 0.001 TYR A 334 ARG 0.006 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3826.93 seconds wall clock time: 68 minutes 52.68 seconds (4132.68 seconds total)