Starting phenix.real_space_refine on Sat Jan 20 07:12:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2p_20239/01_2024/6p2p_20239_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 P 12 5.49 5 S 76 5.16 5 C 9464 2.51 5 N 2174 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 494": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 401": "NH1" <-> "NH2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 494": "NH1" <-> "NH2" Residue "D ARG 525": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13952 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3427 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3415 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3427 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3415 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.42, per 1000 atoms: 0.53 Number of scatterers: 13952 At special positions: 0 Unit cell: (206.09, 116.97, 79.094, 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 76 16.00 P 12 15.00 O 2226 8.00 N 2174 7.00 C 9464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.7 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 0 sheets defined 69.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 181 through 209 Proline residue: A 199 - end of helix removed outlier: 4.069A pdb=" N GLY A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 250 through 272 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.569A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.104A pdb=" N TYR A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 354 removed outlier: 4.031A pdb=" N ALA A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 370 through 396 removed outlier: 4.066A pdb=" N TRP A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) 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 422 through 440 removed outlier: 4.248A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 497 through 523 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 136 through 163 removed outlier: 3.915A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 181 through 208 Proline residue: B 199 - end of helix removed outlier: 3.553A pdb=" N THR B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 252 through 272 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.163A pdb=" N TYR B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 354 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 387 through 395 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 422 through 439 removed outlier: 4.721A pdb=" N LYS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 468 removed outlier: 3.743A pdb=" N LYS B 445 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER B 446 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 466 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.780A pdb=" N PHE B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 477 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 523 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 181 through 209 Proline residue: C 199 - end of helix removed outlier: 4.069A pdb=" N GLY C 209 " --> pdb=" O HIS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 234 Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 250 through 272 Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.569A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 280' Processing helix chain 'C' and resid 294 through 302 removed outlier: 4.104A pdb=" N TYR C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 354 removed outlier: 4.031A pdb=" N ALA C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 363 through 366 No H-bonds generated for 'chain 'C' and resid 363 through 366' Processing helix chain 'C' and resid 370 through 396 removed outlier: 4.066A pdb=" N TRP C 388 " --> pdb=" O PHE C 384 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 422 through 440 removed outlier: 4.248A pdb=" N LYS C 434 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP C 435 " --> pdb=" O TYR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 468 Processing helix chain 'C' and resid 474 through 490 Processing helix chain 'C' and resid 497 through 523 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 136 through 163 removed outlier: 3.915A pdb=" N ILE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 181 through 208 Proline residue: D 199 - end of helix removed outlier: 3.554A pdb=" N THR D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 252 through 272 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 294 through 302 removed outlier: 4.163A pdb=" N TYR D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 354 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 387 through 395 Processing helix chain 'D' and resid 407 through 409 No H-bonds generated for 'chain 'D' and resid 407 through 409' Processing helix chain 'D' and resid 422 through 439 removed outlier: 4.721A pdb=" N LYS D 434 " --> pdb=" O TYR D 430 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 468 removed outlier: 3.743A pdb=" N LYS D 445 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 446 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 459 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 466 " --> pdb=" O ALA D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 490 removed outlier: 3.780A pdb=" N PHE D 476 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 477 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 523 798 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2370 1.33 - 1.45: 4504 1.45 - 1.57: 7468 1.57 - 1.69: 20 1.69 - 1.81: 124 Bond restraints: 14486 Sorted by residual: bond pdb=" C49 3VV B 700 " pdb=" C50 3VV B 700 " ideal model delta sigma weight residual 1.291 1.524 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C49 3VV D 700 " pdb=" C50 3VV D 700 " ideal model delta sigma weight residual 1.291 1.524 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C49 3VV C 700 " pdb=" C50 3VV C 700 " ideal model delta sigma weight residual 1.291 1.520 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C49 3VV A 700 " pdb=" C50 3VV A 700 " ideal model delta sigma weight residual 1.291 1.520 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C49 3VV C 700 " pdb=" O48 3VV C 700 " ideal model delta sigma weight residual 1.621 1.409 0.212 2.00e-02 2.50e+03 1.13e+02 ... (remaining 14481 not shown) Histogram of bond angle deviations from ideal: 77.03 - 88.44: 4 88.44 - 99.85: 8 99.85 - 111.26: 5869 111.26 - 122.68: 12853 122.68 - 134.09: 1004 Bond angle restraints: 19738 Sorted by residual: angle pdb=" O37 3VV A 700 " pdb=" P38 3VV A 700 " pdb=" O40 3VV A 700 " ideal model delta sigma weight residual 109.48 77.03 32.45 3.00e+00 1.11e-01 1.17e+02 angle pdb=" O37 3VV C 700 " pdb=" P38 3VV C 700 " pdb=" O40 3VV C 700 " ideal model delta sigma weight residual 109.48 77.06 32.42 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C09 3VV C 700 " pdb=" C10 3VV C 700 " pdb=" C11 3VV C 700 " ideal model delta sigma weight residual 152.65 124.50 28.15 3.00e+00 1.11e-01 8.81e+01 angle pdb=" C09 3VV A 700 " pdb=" C10 3VV A 700 " pdb=" C11 3VV A 700 " ideal model delta sigma weight residual 152.65 124.50 28.15 3.00e+00 1.11e-01 8.81e+01 angle pdb=" C09 3VV B 700 " pdb=" C10 3VV B 700 " pdb=" C11 3VV B 700 " ideal model delta sigma weight residual 152.65 125.66 26.99 3.00e+00 1.11e-01 8.09e+01 ... (remaining 19733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 7428 24.91 - 49.82: 564 49.82 - 74.72: 66 74.72 - 99.63: 18 99.63 - 124.54: 6 Dihedral angle restraints: 8082 sinusoidal: 3212 harmonic: 4870 Sorted by residual: dihedral pdb=" CA LEU C 167 " pdb=" C LEU C 167 " pdb=" N VAL C 168 " pdb=" CA VAL C 168 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA LEU A 167 " pdb=" C LEU A 167 " pdb=" N VAL A 168 " pdb=" CA VAL A 168 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA VAL C 361 " pdb=" C VAL C 361 " pdb=" N LEU C 362 " pdb=" CA LEU C 362 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 8079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1789 0.071 - 0.141: 251 0.141 - 0.212: 14 0.212 - 0.282: 10 0.282 - 0.353: 6 Chirality restraints: 2070 Sorted by residual: chirality pdb=" C31 3VV C 700 " pdb=" C29 3VV C 700 " pdb=" C33 3VV C 700 " pdb=" O32 3VV C 700 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C31 3VV A 700 " pdb=" C29 3VV A 700 " pdb=" C33 3VV A 700 " pdb=" O32 3VV A 700 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C52 3VV C 700 " pdb=" C47 3VV C 700 " pdb=" C50 3VV C 700 " pdb=" O53 3VV C 700 " both_signs ideal model delta sigma weight residual False 2.56 2.91 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 2067 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 3VV D 700 " 0.254 2.00e-02 2.50e+03 2.18e-01 5.92e+02 pdb=" C29 3VV D 700 " -0.058 2.00e-02 2.50e+03 pdb=" C31 3VV D 700 " -0.025 2.00e-02 2.50e+03 pdb=" N28 3VV D 700 " -0.362 2.00e-02 2.50e+03 pdb=" O30 3VV D 700 " 0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 3VV B 700 " -0.254 2.00e-02 2.50e+03 2.17e-01 5.91e+02 pdb=" C29 3VV B 700 " 0.058 2.00e-02 2.50e+03 pdb=" C31 3VV B 700 " 0.026 2.00e-02 2.50e+03 pdb=" N28 3VV B 700 " 0.362 2.00e-02 2.50e+03 pdb=" O30 3VV B 700 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 3VV A 700 " -0.175 2.00e-02 2.50e+03 1.43e-01 2.57e+02 pdb=" C29 3VV A 700 " 0.078 2.00e-02 2.50e+03 pdb=" C31 3VV A 700 " -0.137 2.00e-02 2.50e+03 pdb=" N28 3VV A 700 " 0.217 2.00e-02 2.50e+03 pdb=" O30 3VV A 700 " 0.017 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1558 2.74 - 3.28: 14887 3.28 - 3.82: 23305 3.82 - 4.36: 26187 4.36 - 4.90: 44395 Nonbonded interactions: 110332 Sorted by model distance: nonbonded pdb=" NZ LYS A 120 " pdb=" OD2 ASP A 426 " model vdw 2.202 2.520 nonbonded pdb=" NZ LYS C 120 " pdb=" OD2 ASP C 426 " model vdw 2.202 2.520 nonbonded pdb=" O ARG B 314 " pdb=" O ASN B 315 " model vdw 2.221 3.040 nonbonded pdb=" O ARG D 314 " pdb=" O ASN D 315 " model vdw 2.221 3.040 nonbonded pdb=" O ALA C 393 " pdb=" N ARG C 397 " model vdw 2.270 2.520 ... (remaining 110327 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' and (resid 118 through 274 or (resid 275 and (name N or name CA or na \ me C or name O or name CB )) or resid 276 through 281 or (resid 287 through 289 \ and (name N or name CA or name C or name O or name CB )) or resid 290 through 52 \ 8 or resid 700)) selection = (chain 'B' and (resid 118 through 286 or resid 288 through 290 or (resid 291 and \ (name N or name CA or name C or name O or name CB )) or resid 292 through 491 o \ r (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 93 through 528 or resid 700)) selection = (chain 'C' and (resid 118 through 274 or (resid 275 and (name N or name CA or na \ me C or name O or name CB )) or resid 276 through 281 or (resid 287 through 289 \ and (name N or name CA or name C or name O or name CB )) or resid 290 through 52 \ 8 or resid 700)) selection = (chain 'D' and (resid 118 through 286 or resid 288 through 290 or (resid 291 and \ (name N or name CA or name C or name O or name CB )) or resid 292 through 491 o \ r (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 93 through 528 or resid 700)) } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.430 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 39.930 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.010 0.233 14486 Z= 0.648 Angle : 1.245 32.454 19738 Z= 0.584 Chirality : 0.054 0.353 2070 Planarity : 0.010 0.218 2372 Dihedral : 17.310 124.541 4942 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.81 % Favored : 91.82 % Rotamer: Outliers : 3.06 % Allowed : 6.13 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.18), residues: 1614 helix: -1.62 (0.13), residues: 1146 sheet: None (None), residues: 0 loop : -3.82 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 206 HIS 0.007 0.001 HIS D 215 PHE 0.023 0.002 PHE B 203 TYR 0.026 0.002 TYR C 523 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9022 (tp) cc_final: 0.8712 (tt) REVERT: A 223 HIS cc_start: 0.7475 (t-90) cc_final: 0.7261 (t-170) REVERT: A 241 TYR cc_start: 0.7065 (t80) cc_final: 0.6784 (t80) REVERT: A 348 LEU cc_start: 0.7621 (tp) cc_final: 0.7397 (mt) REVERT: A 357 PHE cc_start: 0.4405 (t80) cc_final: 0.3279 (m-80) REVERT: A 395 MET cc_start: 0.8425 (mtm) cc_final: 0.8204 (mtm) REVERT: A 406 ASP cc_start: 0.8782 (p0) cc_final: 0.8446 (p0) REVERT: A 471 PHE cc_start: 0.7089 (t80) cc_final: 0.6865 (t80) REVERT: A 480 MET cc_start: 0.8622 (mmm) cc_final: 0.8328 (mmm) REVERT: B 228 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.6853 (mmt) REVERT: C 202 LEU cc_start: 0.9025 (tp) cc_final: 0.8729 (tt) REVERT: C 241 TYR cc_start: 0.7068 (t80) cc_final: 0.6790 (t80) REVERT: C 348 LEU cc_start: 0.7623 (tp) cc_final: 0.7397 (mt) REVERT: C 357 PHE cc_start: 0.4438 (t80) cc_final: 0.3296 (m-80) REVERT: C 395 MET cc_start: 0.8422 (mtm) cc_final: 0.8201 (mtm) REVERT: C 406 ASP cc_start: 0.8787 (p0) cc_final: 0.8452 (p0) REVERT: C 471 PHE cc_start: 0.7087 (t80) cc_final: 0.6863 (t80) REVERT: C 480 MET cc_start: 0.8617 (mmm) cc_final: 0.8315 (mmm) REVERT: D 228 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.6861 (mmt) outliers start: 44 outliers final: 24 residues processed: 364 average time/residue: 0.2657 time to fit residues: 138.2502 Evaluate side-chains 271 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 296 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 223 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 450 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 280 ASN A 295 ASN A 315 ASN A 351 ASN A 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 137 HIS B 215 HIS C 260 GLN C 280 ASN C 295 ASN C 315 ASN C 351 ASN C 390 ASN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 137 HIS D 215 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14486 Z= 0.201 Angle : 0.630 10.137 19738 Z= 0.329 Chirality : 0.042 0.212 2070 Planarity : 0.006 0.052 2372 Dihedral : 12.500 97.009 2022 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 3.55 % Allowed : 15.74 % Favored : 80.71 % 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: -1.60 (0.19), residues: 1614 helix: -0.23 (0.14), residues: 1178 sheet: None (None), residues: 0 loop : -3.25 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 438 HIS 0.004 0.001 HIS B 215 PHE 0.015 0.001 PHE D 203 TYR 0.014 0.001 TYR A 308 ARG 0.002 0.000 ARG C 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.8877 (tmm) cc_final: 0.6815 (mmt) REVERT: A 406 ASP cc_start: 0.8240 (p0) cc_final: 0.7740 (p0) REVERT: A 471 PHE cc_start: 0.7165 (t80) cc_final: 0.6676 (m-80) REVERT: A 480 MET cc_start: 0.8509 (mmm) cc_final: 0.8282 (mmm) REVERT: B 120 LYS cc_start: 0.7033 (tttm) cc_final: 0.6716 (tmtt) REVERT: B 131 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: B 228 MET cc_start: 0.8648 (ttm) cc_final: 0.7481 (mmt) REVERT: B 456 SER cc_start: 0.8980 (t) cc_final: 0.8422 (p) REVERT: C 228 MET cc_start: 0.8879 (tmm) cc_final: 0.6816 (mmt) REVERT: C 241 TYR cc_start: 0.6949 (t80) cc_final: 0.6729 (t80) REVERT: C 406 ASP cc_start: 0.8247 (p0) cc_final: 0.7747 (p0) REVERT: C 471 PHE cc_start: 0.7164 (t80) cc_final: 0.6679 (m-80) REVERT: C 480 MET cc_start: 0.8502 (mmm) cc_final: 0.8271 (mmm) REVERT: D 120 LYS cc_start: 0.7039 (tttm) cc_final: 0.6716 (tmtt) REVERT: D 131 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: D 228 MET cc_start: 0.8613 (ttm) cc_final: 0.7464 (mmt) REVERT: D 456 SER cc_start: 0.8977 (t) cc_final: 0.8417 (p) outliers start: 51 outliers final: 31 residues processed: 312 average time/residue: 0.2022 time to fit residues: 99.3528 Evaluate side-chains 278 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 479 PHE Chi-restraints excluded: chain D residue 482 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 0.0170 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN B 315 ASN B 409 ASN C 223 HIS C 260 GLN C 329 GLN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 315 ASN D 409 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14486 Z= 0.296 Angle : 0.648 7.684 19738 Z= 0.342 Chirality : 0.045 0.266 2070 Planarity : 0.006 0.066 2372 Dihedral : 11.538 96.785 1968 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.25 % Favored : 92.63 % Rotamer: Outliers : 5.01 % Allowed : 18.80 % Favored : 76.18 % 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: -1.14 (0.20), residues: 1614 helix: 0.12 (0.14), residues: 1158 sheet: None (None), residues: 0 loop : -2.97 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 438 HIS 0.015 0.001 HIS D 215 PHE 0.021 0.002 PHE D 203 TYR 0.018 0.002 TYR D 142 ARG 0.003 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 259 time to evaluate : 1.572 Fit side-chains REVERT: A 395 MET cc_start: 0.8474 (mtm) cc_final: 0.8207 (mtm) REVERT: A 406 ASP cc_start: 0.8573 (p0) cc_final: 0.8093 (p0) REVERT: A 471 PHE cc_start: 0.7102 (t80) cc_final: 0.6800 (m-80) REVERT: B 120 LYS cc_start: 0.6810 (tttm) cc_final: 0.6544 (tmtt) REVERT: B 130 ASP cc_start: 0.8213 (t0) cc_final: 0.7856 (t0) REVERT: B 349 PHE cc_start: 0.7237 (m-10) cc_final: 0.6995 (m-10) REVERT: C 241 TYR cc_start: 0.6967 (t80) cc_final: 0.6755 (t80) REVERT: C 395 MET cc_start: 0.8471 (mtm) cc_final: 0.8209 (mtm) REVERT: C 406 ASP cc_start: 0.8571 (p0) cc_final: 0.8091 (p0) REVERT: C 471 PHE cc_start: 0.7098 (t80) cc_final: 0.6801 (m-80) REVERT: D 120 LYS cc_start: 0.6812 (tttm) cc_final: 0.6542 (tmtt) REVERT: D 130 ASP cc_start: 0.8213 (t0) cc_final: 0.7857 (t0) REVERT: D 257 ILE cc_start: 0.9120 (tt) cc_final: 0.8834 (tt) outliers start: 72 outliers final: 54 residues processed: 296 average time/residue: 0.2015 time to fit residues: 93.7460 Evaluate side-chains 289 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 482 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.0010 chunk 41 optimal weight: 0.0770 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN B 118 GLN B 215 HIS B 260 GLN B 409 ASN C 390 ASN D 118 GLN D 215 HIS D 260 GLN D 409 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14486 Z= 0.150 Angle : 0.588 10.100 19738 Z= 0.300 Chirality : 0.040 0.197 2070 Planarity : 0.005 0.059 2372 Dihedral : 10.714 94.432 1964 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.70 % Favored : 94.18 % Rotamer: Outliers : 5.36 % Allowed : 20.33 % Favored : 74.30 % 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: -0.49 (0.21), residues: 1614 helix: 0.53 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -2.62 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 388 HIS 0.008 0.001 HIS D 215 PHE 0.016 0.001 PHE D 331 TYR 0.017 0.001 TYR D 142 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 273 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8982 (tmm) cc_final: 0.6861 (mmt) REVERT: A 338 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5837 (t80) REVERT: A 395 MET cc_start: 0.8449 (mtm) cc_final: 0.8187 (mtm) REVERT: A 406 ASP cc_start: 0.8255 (p0) cc_final: 0.7735 (p0) REVERT: B 120 LYS cc_start: 0.6713 (tttm) cc_final: 0.6376 (tmtt) REVERT: B 131 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: B 228 MET cc_start: 0.8591 (ttm) cc_final: 0.7443 (mmt) REVERT: B 257 ILE cc_start: 0.9084 (tt) cc_final: 0.8807 (tt) REVERT: B 456 SER cc_start: 0.8896 (t) cc_final: 0.8371 (p) REVERT: C 228 MET cc_start: 0.8979 (tmm) cc_final: 0.6853 (mmt) REVERT: C 338 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5836 (t80) REVERT: C 395 MET cc_start: 0.8445 (mtm) cc_final: 0.8187 (mtm) REVERT: C 406 ASP cc_start: 0.8252 (p0) cc_final: 0.7735 (p0) REVERT: D 120 LYS cc_start: 0.6719 (tttm) cc_final: 0.6377 (tmtt) REVERT: D 131 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: D 228 MET cc_start: 0.8591 (ttm) cc_final: 0.7446 (mmt) REVERT: D 257 ILE cc_start: 0.9066 (tt) cc_final: 0.8794 (tt) REVERT: D 456 SER cc_start: 0.8911 (t) cc_final: 0.8341 (p) outliers start: 77 outliers final: 51 residues processed: 325 average time/residue: 0.2143 time to fit residues: 107.3706 Evaluate side-chains 305 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 250 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14486 Z= 0.199 Angle : 0.592 8.700 19738 Z= 0.304 Chirality : 0.041 0.196 2070 Planarity : 0.005 0.060 2372 Dihedral : 10.485 92.424 1964 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.57 % Allowed : 21.94 % Favored : 72.49 % 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: -0.26 (0.21), residues: 1614 helix: 0.72 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -2.52 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 438 HIS 0.008 0.001 HIS B 215 PHE 0.018 0.001 PHE C 335 TYR 0.017 0.001 TYR D 142 ARG 0.002 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 253 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8991 (tp) cc_final: 0.8789 (tt) REVERT: A 338 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6223 (t80) REVERT: A 395 MET cc_start: 0.8435 (mtm) cc_final: 0.8183 (mtm) REVERT: A 406 ASP cc_start: 0.8292 (p0) cc_final: 0.7731 (p0) REVERT: B 120 LYS cc_start: 0.6772 (tttm) cc_final: 0.6489 (tmtt) REVERT: B 131 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: B 257 ILE cc_start: 0.9103 (tt) cc_final: 0.8814 (tt) REVERT: B 484 MET cc_start: 0.7464 (tmm) cc_final: 0.6950 (tmm) REVERT: C 228 MET cc_start: 0.8948 (tmm) cc_final: 0.6887 (mmt) REVERT: C 338 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6225 (t80) REVERT: C 395 MET cc_start: 0.8433 (mtm) cc_final: 0.8187 (mtm) REVERT: C 406 ASP cc_start: 0.8285 (p0) cc_final: 0.7727 (p0) REVERT: D 120 LYS cc_start: 0.6769 (tttm) cc_final: 0.6488 (tmtt) REVERT: D 131 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: D 257 ILE cc_start: 0.9106 (tt) cc_final: 0.8815 (tt) REVERT: D 456 SER cc_start: 0.8888 (t) cc_final: 0.8370 (p) REVERT: D 484 MET cc_start: 0.7460 (tmm) cc_final: 0.6943 (tmm) outliers start: 80 outliers final: 65 residues processed: 305 average time/residue: 0.2035 time to fit residues: 97.9365 Evaluate side-chains 309 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 240 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.6980 chunk 139 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14486 Z= 0.149 Angle : 0.571 10.914 19738 Z= 0.288 Chirality : 0.040 0.201 2070 Planarity : 0.005 0.056 2372 Dihedral : 10.090 89.962 1964 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.08 % Allowed : 22.49 % Favored : 72.42 % 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: -0.05 (0.21), residues: 1614 helix: 0.89 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -2.51 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 388 HIS 0.006 0.001 HIS D 215 PHE 0.017 0.001 PHE C 335 TYR 0.016 0.001 TYR D 142 ARG 0.001 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 270 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8972 (tp) cc_final: 0.8766 (tt) REVERT: A 228 MET cc_start: 0.8939 (tmm) cc_final: 0.6993 (mmt) REVERT: A 338 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.6234 (t80) REVERT: A 392 PHE cc_start: 0.8421 (m-10) cc_final: 0.8207 (m-80) REVERT: A 395 MET cc_start: 0.8390 (mtm) cc_final: 0.8125 (mtm) REVERT: A 406 ASP cc_start: 0.8153 (p0) cc_final: 0.7592 (p0) REVERT: A 480 MET cc_start: 0.8600 (mmm) cc_final: 0.8240 (mmm) REVERT: B 120 LYS cc_start: 0.6851 (tttm) cc_final: 0.6520 (tmtt) REVERT: B 131 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: B 257 ILE cc_start: 0.9100 (tt) cc_final: 0.8815 (tt) REVERT: B 484 MET cc_start: 0.7407 (tmm) cc_final: 0.6906 (tmm) REVERT: C 338 TYR cc_start: 0.6535 (OUTLIER) cc_final: 0.6235 (t80) REVERT: C 392 PHE cc_start: 0.8422 (m-10) cc_final: 0.8210 (m-80) REVERT: C 395 MET cc_start: 0.8384 (mtm) cc_final: 0.8121 (mtm) REVERT: C 406 ASP cc_start: 0.8143 (p0) cc_final: 0.7584 (p0) REVERT: C 480 MET cc_start: 0.8604 (mmm) cc_final: 0.8247 (mmm) REVERT: C 482 PHE cc_start: 0.8080 (m-10) cc_final: 0.7784 (m-80) REVERT: D 120 LYS cc_start: 0.6851 (tttm) cc_final: 0.6520 (tmtt) REVERT: D 131 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7633 (pt0) REVERT: D 257 ILE cc_start: 0.9087 (tt) cc_final: 0.8804 (tt) REVERT: D 456 SER cc_start: 0.8834 (t) cc_final: 0.8301 (p) REVERT: D 484 MET cc_start: 0.7393 (tmm) cc_final: 0.6893 (tmm) outliers start: 73 outliers final: 59 residues processed: 319 average time/residue: 0.2021 time to fit residues: 101.2000 Evaluate side-chains 312 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 249 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 0.0070 chunk 86 optimal weight: 0.1980 chunk 154 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN C 260 GLN D 118 GLN D 215 HIS D 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14486 Z= 0.148 Angle : 0.584 9.885 19738 Z= 0.290 Chirality : 0.040 0.213 2070 Planarity : 0.005 0.055 2372 Dihedral : 9.751 88.941 1964 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.87 % Allowed : 23.26 % Favored : 71.87 % 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: 0.10 (0.21), residues: 1614 helix: 1.01 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -2.46 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 388 HIS 0.005 0.001 HIS D 215 PHE 0.022 0.001 PHE A 171 TYR 0.017 0.001 TYR C 142 ARG 0.001 0.000 ARG C 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 264 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8914 (tmm) cc_final: 0.6883 (mmt) REVERT: A 338 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6286 (t80) REVERT: A 392 PHE cc_start: 0.8295 (m-10) cc_final: 0.8092 (m-80) REVERT: A 395 MET cc_start: 0.8386 (mtm) cc_final: 0.8134 (mtm) REVERT: A 406 ASP cc_start: 0.8084 (p0) cc_final: 0.7483 (p0) REVERT: A 480 MET cc_start: 0.8573 (mmm) cc_final: 0.8355 (mmm) REVERT: B 120 LYS cc_start: 0.6886 (tttm) cc_final: 0.6509 (tmtt) REVERT: B 131 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: B 257 ILE cc_start: 0.9095 (tt) cc_final: 0.8813 (tt) REVERT: B 484 MET cc_start: 0.7439 (tmm) cc_final: 0.6945 (tmm) REVERT: C 228 MET cc_start: 0.8932 (tmm) cc_final: 0.7019 (mmt) REVERT: C 338 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6317 (t80) REVERT: C 392 PHE cc_start: 0.8291 (m-10) cc_final: 0.8090 (m-80) REVERT: C 395 MET cc_start: 0.8383 (mtm) cc_final: 0.8133 (mtm) REVERT: C 406 ASP cc_start: 0.8057 (p0) cc_final: 0.7475 (p0) REVERT: C 480 MET cc_start: 0.8559 (mmm) cc_final: 0.8341 (mmm) REVERT: D 120 LYS cc_start: 0.6888 (tttm) cc_final: 0.6509 (tmtt) REVERT: D 131 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: D 257 ILE cc_start: 0.9083 (tt) cc_final: 0.8789 (tt) REVERT: D 456 SER cc_start: 0.8782 (t) cc_final: 0.8245 (p) REVERT: D 484 MET cc_start: 0.7435 (tmm) cc_final: 0.6931 (tmm) outliers start: 70 outliers final: 59 residues processed: 309 average time/residue: 0.2027 time to fit residues: 99.0465 Evaluate side-chains 310 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 247 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN B 351 ASN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 260 GLN D 351 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14486 Z= 0.186 Angle : 0.619 14.955 19738 Z= 0.303 Chirality : 0.041 0.199 2070 Planarity : 0.005 0.056 2372 Dihedral : 9.625 89.710 1964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.43 % Allowed : 23.26 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1614 helix: 0.99 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -2.32 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 438 HIS 0.008 0.001 HIS D 215 PHE 0.019 0.001 PHE A 171 TYR 0.020 0.001 TYR B 142 ARG 0.002 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 248 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8894 (tmm) cc_final: 0.6889 (mmt) REVERT: A 392 PHE cc_start: 0.8382 (m-10) cc_final: 0.8174 (m-80) REVERT: A 395 MET cc_start: 0.8385 (mtm) cc_final: 0.8130 (mtm) REVERT: A 406 ASP cc_start: 0.8275 (p0) cc_final: 0.7695 (p0) REVERT: A 480 MET cc_start: 0.8539 (mmm) cc_final: 0.8302 (mmm) REVERT: B 120 LYS cc_start: 0.6890 (tttm) cc_final: 0.6511 (tmtt) REVERT: B 257 ILE cc_start: 0.9116 (tt) cc_final: 0.8828 (tt) REVERT: B 484 MET cc_start: 0.7441 (tmm) cc_final: 0.6900 (tmm) REVERT: C 228 MET cc_start: 0.8947 (tmm) cc_final: 0.6947 (mmt) REVERT: C 392 PHE cc_start: 0.8379 (m-10) cc_final: 0.8170 (m-80) REVERT: C 395 MET cc_start: 0.8381 (mtm) cc_final: 0.8128 (mtm) REVERT: C 406 ASP cc_start: 0.8272 (p0) cc_final: 0.7689 (p0) REVERT: C 480 MET cc_start: 0.8529 (mmm) cc_final: 0.8288 (mmm) REVERT: D 120 LYS cc_start: 0.6890 (tttm) cc_final: 0.6481 (tmtt) REVERT: D 257 ILE cc_start: 0.9089 (tt) cc_final: 0.8799 (tt) REVERT: D 484 MET cc_start: 0.7431 (tmm) cc_final: 0.6892 (tmm) outliers start: 78 outliers final: 66 residues processed: 301 average time/residue: 0.2085 time to fit residues: 98.5876 Evaluate side-chains 307 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 241 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.3980 chunk 147 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 0.0020 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 0.3980 chunk 135 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14486 Z= 0.145 Angle : 0.607 14.573 19738 Z= 0.292 Chirality : 0.040 0.210 2070 Planarity : 0.005 0.053 2372 Dihedral : 9.105 89.190 1958 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.11 % Allowed : 24.58 % Favored : 71.31 % 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: 0.27 (0.21), residues: 1614 helix: 1.14 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 388 HIS 0.010 0.001 HIS D 215 PHE 0.017 0.001 PHE D 331 TYR 0.020 0.001 TYR B 142 ARG 0.002 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 275 time to evaluate : 1.675 Fit side-chains REVERT: A 228 MET cc_start: 0.8867 (tmm) cc_final: 0.6903 (mmt) REVERT: A 395 MET cc_start: 0.8381 (mtm) cc_final: 0.8171 (mtm) REVERT: A 406 ASP cc_start: 0.8005 (p0) cc_final: 0.7414 (p0) REVERT: A 480 MET cc_start: 0.8492 (mmm) cc_final: 0.8252 (mmm) REVERT: B 120 LYS cc_start: 0.6962 (tttm) cc_final: 0.6619 (tmtt) REVERT: B 180 LYS cc_start: 0.6430 (mptt) cc_final: 0.5649 (mptt) REVERT: B 257 ILE cc_start: 0.9107 (tt) cc_final: 0.8819 (tt) REVERT: B 349 PHE cc_start: 0.7234 (m-10) cc_final: 0.7008 (m-10) REVERT: B 456 SER cc_start: 0.8755 (t) cc_final: 0.8221 (p) REVERT: B 484 MET cc_start: 0.7390 (tmm) cc_final: 0.6836 (tmm) REVERT: C 228 MET cc_start: 0.8923 (tmm) cc_final: 0.6899 (mmt) REVERT: C 395 MET cc_start: 0.8378 (mtm) cc_final: 0.8165 (mtm) REVERT: C 406 ASP cc_start: 0.8000 (p0) cc_final: 0.7410 (p0) REVERT: C 480 MET cc_start: 0.8485 (mmm) cc_final: 0.8245 (mmm) REVERT: D 120 LYS cc_start: 0.6964 (tttm) cc_final: 0.6620 (tmtt) REVERT: D 180 LYS cc_start: 0.6491 (mptt) cc_final: 0.5475 (mptt) REVERT: D 257 ILE cc_start: 0.9080 (tt) cc_final: 0.8798 (tt) REVERT: D 456 SER cc_start: 0.8764 (t) cc_final: 0.8227 (p) REVERT: D 484 MET cc_start: 0.7386 (tmm) cc_final: 0.6851 (tmm) outliers start: 59 outliers final: 52 residues processed: 311 average time/residue: 0.1971 time to fit residues: 97.6157 Evaluate side-chains 316 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 264 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN B 368 ASN B 409 ASN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 260 GLN D 368 ASN D 409 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14486 Z= 0.194 Angle : 0.626 12.529 19738 Z= 0.305 Chirality : 0.041 0.212 2070 Planarity : 0.005 0.055 2372 Dihedral : 9.253 89.711 1958 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.46 % Allowed : 23.75 % Favored : 71.80 % 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 (0.21), residues: 1614 helix: 1.09 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -2.37 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.008 0.001 HIS B 215 PHE 0.018 0.001 PHE D 367 TYR 0.020 0.001 TYR B 142 ARG 0.002 0.000 ARG D 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 255 time to evaluate : 1.457 Fit side-chains REVERT: A 228 MET cc_start: 0.8897 (tmm) cc_final: 0.6927 (mmt) REVERT: A 395 MET cc_start: 0.8389 (mtm) cc_final: 0.8170 (mtm) REVERT: A 406 ASP cc_start: 0.8294 (p0) cc_final: 0.7712 (p0) REVERT: A 480 MET cc_start: 0.8495 (mmm) cc_final: 0.8245 (mmm) REVERT: B 120 LYS cc_start: 0.7140 (tttm) cc_final: 0.6672 (tmtt) REVERT: B 215 HIS cc_start: 0.6088 (OUTLIER) cc_final: 0.5284 (t-90) REVERT: B 257 ILE cc_start: 0.9117 (tt) cc_final: 0.8828 (tt) REVERT: B 349 PHE cc_start: 0.7297 (m-10) cc_final: 0.7051 (m-10) REVERT: B 484 MET cc_start: 0.7427 (tmm) cc_final: 0.6869 (tmm) REVERT: C 228 MET cc_start: 0.8939 (tmm) cc_final: 0.6884 (mmt) REVERT: C 395 MET cc_start: 0.8386 (mtm) cc_final: 0.8165 (mtm) REVERT: C 406 ASP cc_start: 0.8292 (p0) cc_final: 0.7710 (p0) REVERT: C 480 MET cc_start: 0.8491 (mmm) cc_final: 0.8238 (mmm) REVERT: D 120 LYS cc_start: 0.7099 (tttm) cc_final: 0.6635 (tmtt) REVERT: D 215 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.5282 (t-90) REVERT: D 257 ILE cc_start: 0.9101 (tt) cc_final: 0.8805 (tt) REVERT: D 456 SER cc_start: 0.8797 (t) cc_final: 0.8288 (p) REVERT: D 484 MET cc_start: 0.7427 (tmm) cc_final: 0.6886 (tmm) outliers start: 64 outliers final: 53 residues processed: 298 average time/residue: 0.1897 time to fit residues: 90.8237 Evaluate side-chains 309 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 215 HIS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 111 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 390 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 215 HIS B 260 GLN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 215 HIS D 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.149425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126280 restraints weight = 28592.084| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.67 r_work: 0.3610 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14486 Z= 0.158 Angle : 0.616 12.543 19738 Z= 0.297 Chirality : 0.040 0.215 2070 Planarity : 0.005 0.054 2372 Dihedral : 9.122 89.734 1958 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.90 % Allowed : 24.72 % Favored : 71.38 % 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: 0.29 (0.21), residues: 1614 helix: 1.17 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.007 0.001 HIS D 215 PHE 0.018 0.001 PHE D 331 TYR 0.020 0.001 TYR B 142 ARG 0.001 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.71 seconds wall clock time: 58 minutes 10.55 seconds (3490.55 seconds total)