Starting phenix.real_space_refine on Fri Jan 19 13:35:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/01_2024/7das_30626.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/01_2024/7das_30626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/01_2024/7das_30626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/01_2024/7das_30626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/01_2024/7das_30626.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/01_2024/7das_30626.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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 66 5.49 5 S 28 5.16 5 C 7232 2.51 5 N 1847 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 642": "OD1" <-> "OD2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 576": "OD1" <-> "OD2" Residue "B GLU 588": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 642": "OD1" <-> "OD2" Residue "B PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B GLU 653": "OE1" <-> "OE2" 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: 11603 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5418 Classifications: {'peptide': 674} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 645} Chain breaks: 1 Chain: "B" Number of atoms: 5393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5393 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain breaks: 1 Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 792 Classifications: {'RNA': 66} Modifications used: {'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna3p': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 707 Unresolved non-hydrogen angles: 1118 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {' G%rna3p_pur:plan2': 17, ' C%rna3p_pyr:plan': 22, ' A%rna3p_pur:plan2': 15, ' U%rna3p_pyr:plan': 12, ' C%rna3p_pyr:plan2': 22, ' G%rna3p_pur:plan': 17, ' A%rna3p_pur:plan': 15} Unresolved non-hydrogen planarities: 717 Time building chain proxies: 6.38, per 1000 atoms: 0.55 Number of scatterers: 11603 At special positions: 0 Unit cell: (110.7, 110.7, 136.12, 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 28 16.00 P 66 15.00 O 2430 8.00 N 1847 7.00 C 7232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 38 " distance=2.04 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 678 " distance=2.01 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 38 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 678 " distance=2.01 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 697 " distance=2.03 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 Atom "ATOM 10938 O4' U C 19 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2586 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 11.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.230A pdb=" N CYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.578A pdb=" N GLY A 196 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.746A pdb=" N LYS A 273 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.817A pdb=" N TRP A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.657A pdb=" N PHE A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Proline residue: A 633 - end of helix Processing helix chain 'A' and resid 651 through 665 removed outlier: 6.436A pdb=" N TRP A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'B' and resid 92 through 99 removed outlier: 4.230A pdb=" N CYS B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.578A pdb=" N GLY B 196 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.747A pdb=" N LYS B 273 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.818A pdb=" N TRP B 453 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.657A pdb=" N PHE B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 651 through 665 removed outlier: 6.436A pdb=" N TRP B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.515A pdb=" N LEU A 57 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 153 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 177 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 203 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 227 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.539A pdb=" N LEU A 187 " --> pdb=" O GLU A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281 removed outlier: 7.309A pdb=" N LEU A 304 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 328 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 385 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 413 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 437 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 462 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 7.048A pdb=" N GLN A 446 " --> pdb=" O GLN A 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 535 through 537 removed outlier: 6.943A pdb=" N LEU A 536 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 592 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 616 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.515A pdb=" N LEU B 57 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 153 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 177 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 203 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 227 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 187 removed outlier: 3.539A pdb=" N LEU B 187 " --> pdb=" O GLU B 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB2, first strand: chain 'B' and resid 279 through 281 removed outlier: 7.309A pdb=" N LEU B 304 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 328 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU B 385 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 413 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU B 437 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE B 462 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 447 removed outlier: 7.048A pdb=" N GLN B 446 " --> pdb=" O GLN B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 535 through 537 removed outlier: 6.944A pdb=" N LEU B 536 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 592 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 616 " --> pdb=" O ASP B 642 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 240 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: 3.67 Time building geometry restraints manager: 5.34 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: 3345 1.33 - 1.46: 2221 1.46 - 1.58: 6164 1.58 - 1.70: 129 1.70 - 1.82: 36 Bond restraints: 11895 Sorted by residual: bond pdb=" N PRO B 579 " pdb=" CD PRO B 579 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" N PRO A 579 " pdb=" CD PRO A 579 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.96e+01 bond pdb=" O3' G C 10 " pdb=" P A C 11 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 bond pdb=" O3' A C 34 " pdb=" P C C 35 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.40e+01 bond pdb=" O3' G C 13 " pdb=" P G C 14 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.32e+01 ... (remaining 11890 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.13: 518 106.13 - 113.13: 6733 113.13 - 120.13: 4218 120.13 - 127.12: 4714 127.12 - 134.12: 116 Bond angle restraints: 16299 Sorted by residual: angle pdb=" N HIS B 683 " pdb=" CA HIS B 683 " pdb=" C HIS B 683 " ideal model delta sigma weight residual 112.38 103.04 9.34 1.22e+00 6.72e-01 5.86e+01 angle pdb=" N HIS A 683 " pdb=" CA HIS A 683 " pdb=" C HIS A 683 " ideal model delta sigma weight residual 112.38 103.06 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" O3' G C 13 " pdb=" C3' G C 13 " pdb=" C2' G C 13 " ideal model delta sigma weight residual 113.70 125.15 -11.45 1.50e+00 4.44e-01 5.83e+01 angle pdb=" C3' G C 18 " pdb=" C2' G C 18 " pdb=" O2' G C 18 " ideal model delta sigma weight residual 110.70 120.23 -9.53 1.50e+00 4.44e-01 4.03e+01 angle pdb=" C4' G C 238 " pdb=" C3' G C 238 " pdb=" O3' G C 238 " ideal model delta sigma weight residual 113.00 122.27 -9.27 1.50e+00 4.44e-01 3.82e+01 ... (remaining 16294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 7196 33.25 - 66.49: 257 66.49 - 99.74: 35 99.74 - 132.99: 0 132.99 - 166.23: 1 Dihedral angle restraints: 7489 sinusoidal: 3526 harmonic: 3963 Sorted by residual: dihedral pdb=" C5' U C 259 " pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" O3' U C 259 " ideal model delta sinusoidal sigma weight residual 82.00 166.04 -84.04 1 8.00e+00 1.56e-02 1.34e+02 dihedral pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" C2' U C 259 " pdb=" C1' U C 259 " ideal model delta sinusoidal sigma weight residual 36.00 -40.89 76.89 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" O4' U C 259 " pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" C2' U C 259 " ideal model delta sinusoidal sigma weight residual -35.00 37.98 -72.98 1 8.00e+00 1.56e-02 1.06e+02 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 1947 0.177 - 0.355: 41 0.355 - 0.532: 3 0.532 - 0.710: 1 0.710 - 0.887: 2 Chirality restraints: 1994 Sorted by residual: chirality pdb=" C3' G C 13 " pdb=" C4' G C 13 " pdb=" O3' G C 13 " pdb=" C2' G C 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.59 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C3' G C 18 " pdb=" C4' G C 18 " pdb=" O3' G C 18 " pdb=" C2' G C 18 " both_signs ideal model delta sigma weight residual False -2.48 -1.69 -0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C2' G C 18 " pdb=" C3' G C 18 " pdb=" O2' G C 18 " pdb=" C1' G C 18 " both_signs ideal model delta sigma weight residual False -2.75 -2.08 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 1991 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 513 " -0.025 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C ASP B 513 " 0.090 2.00e-02 2.50e+03 pdb=" O ASP B 513 " -0.034 2.00e-02 2.50e+03 pdb=" N LEU B 514 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 513 " 0.025 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C ASP A 513 " -0.090 2.00e-02 2.50e+03 pdb=" O ASP A 513 " 0.034 2.00e-02 2.50e+03 pdb=" N LEU A 514 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 678 " -0.025 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C CYS B 678 " 0.089 2.00e-02 2.50e+03 pdb=" O CYS B 678 " -0.033 2.00e-02 2.50e+03 pdb=" N ASN B 679 " -0.030 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 4 2.18 - 2.86: 4267 2.86 - 3.54: 15216 3.54 - 4.22: 26677 4.22 - 4.90: 45075 Nonbonded interactions: 91239 Sorted by model distance: nonbonded pdb=" ND2 ASN B 518 " pdb=" O4' U C 19 " model vdw 1.496 2.520 nonbonded pdb=" OD1 ASN B 542 " pdb=" O2' U C 17 " model vdw 1.898 2.440 nonbonded pdb=" ND2 ASN B 518 " pdb=" C1' U C 19 " model vdw 1.977 3.550 nonbonded pdb=" CG ASN B 518 " pdb=" O4' U C 19 " model vdw 2.175 3.270 nonbonded pdb=" O PRO A 316 " pdb=" NE1 TRP A 354 " model vdw 2.213 2.520 ... (remaining 91234 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 24 through 697) selection = chain 'B' } 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 group one per residue 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: 4.420 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: 0.000 Extract box with map and model: 23.350 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.240 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.006 0.062 11895 Z= 0.372 Angle : 0.918 11.450 16299 Z= 0.594 Chirality : 0.071 0.887 1994 Planarity : 0.005 0.052 1922 Dihedral : 16.736 166.233 4879 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.93 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.87 (0.20), residues: 1337 helix: -3.01 (0.41), residues: 88 sheet: -2.94 (0.34), residues: 192 loop : -2.69 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 547 HIS 0.005 0.001 HIS A 109 PHE 0.018 0.001 PHE B 558 TYR 0.017 0.002 TYR B 469 ARG 0.011 0.001 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 643 MET cc_start: 0.7938 (ttm) cc_final: 0.7446 (mtp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3249 time to fit residues: 48.4230 Evaluate side-chains 39 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 110 ASN A 134 ASN A 170 GLN A 260 GLN A 395 GLN A 446 GLN A 467 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS A 573 ASN A 585 ASN A 610 GLN A 621 ASN A 646 ASN A 679 ASN B 61 HIS B 62 ASN B 109 HIS B 110 ASN B 134 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 170 GLN B 175 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 446 GLN B 467 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS B 573 ASN B 585 ASN B 610 GLN B 621 ASN B 639 ASN B 646 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11895 Z= 0.225 Angle : 0.574 9.688 16299 Z= 0.295 Chirality : 0.041 0.143 1994 Planarity : 0.004 0.037 1922 Dihedral : 14.160 178.620 2221 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.27 % Allowed : 10.10 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.71 (0.22), residues: 1337 helix: -0.98 (0.57), residues: 88 sheet: -2.52 (0.37), residues: 189 loop : -1.89 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 547 HIS 0.004 0.001 HIS B 109 PHE 0.011 0.001 PHE B 460 TYR 0.015 0.001 TYR B 469 ARG 0.006 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 PHE cc_start: 0.8401 (t80) cc_final: 0.8098 (t80) REVERT: A 539 GLN cc_start: 0.8377 (mp10) cc_final: 0.7537 (mp10) REVERT: B 643 MET cc_start: 0.7974 (ttm) cc_final: 0.7495 (mtp) outliers start: 16 outliers final: 8 residues processed: 53 average time/residue: 0.2289 time to fit residues: 18.9757 Evaluate side-chains 40 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 567 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 146 ASN B 451 GLN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11895 Z= 0.198 Angle : 0.512 8.427 16299 Z= 0.265 Chirality : 0.040 0.145 1994 Planarity : 0.004 0.037 1922 Dihedral : 13.573 170.314 2221 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.19 % Allowed : 12.65 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.28 (0.23), residues: 1337 helix: -0.72 (0.59), residues: 88 sheet: -2.50 (0.38), residues: 202 loop : -1.48 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.003 0.001 HIS A 109 PHE 0.010 0.001 PHE A 538 TYR 0.014 0.001 TYR B 469 ARG 0.004 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 484 GLN cc_start: 0.7617 (tt0) cc_final: 0.7332 (mt0) REVERT: B 643 MET cc_start: 0.7975 (ttm) cc_final: 0.7487 (mtp) outliers start: 15 outliers final: 7 residues processed: 45 average time/residue: 0.2140 time to fit residues: 15.7334 Evaluate side-chains 30 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 567 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN B 106 ASN ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11895 Z= 0.309 Angle : 0.582 7.581 16299 Z= 0.299 Chirality : 0.042 0.161 1994 Planarity : 0.004 0.039 1922 Dihedral : 13.882 162.503 2221 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 1.75 % Allowed : 14.40 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.45 (0.23), residues: 1337 helix: -1.29 (0.52), residues: 106 sheet: -2.50 (0.40), residues: 188 loop : -1.60 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 274 HIS 0.013 0.001 HIS B 682 PHE 0.014 0.001 PHE B 460 TYR 0.016 0.002 TYR A 469 ARG 0.003 0.001 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 33 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7863 (p90) REVERT: A 512 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 484 GLN cc_start: 0.7696 (tt0) cc_final: 0.7323 (tm-30) outliers start: 22 outliers final: 13 residues processed: 53 average time/residue: 0.1852 time to fit residues: 16.6729 Evaluate side-chains 40 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 25 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 567 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11895 Z= 0.210 Angle : 0.508 7.400 16299 Z= 0.262 Chirality : 0.040 0.169 1994 Planarity : 0.003 0.040 1922 Dihedral : 13.769 163.672 2221 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.99 % Allowed : 15.43 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.21 (0.24), residues: 1337 helix: -1.03 (0.55), residues: 100 sheet: -2.43 (0.41), residues: 188 loop : -1.42 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.002 0.000 HIS A 540 PHE 0.009 0.001 PHE B 460 TYR 0.013 0.001 TYR A 469 ARG 0.003 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 28 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7579 (p90) REVERT: A 512 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8531 (tt) REVERT: B 484 GLN cc_start: 0.7680 (tt0) cc_final: 0.7368 (tm-30) outliers start: 25 outliers final: 18 residues processed: 51 average time/residue: 0.1670 time to fit residues: 14.9989 Evaluate side-chains 44 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 24 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 697 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN B 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11895 Z= 0.288 Angle : 0.562 7.410 16299 Z= 0.288 Chirality : 0.042 0.154 1994 Planarity : 0.004 0.042 1922 Dihedral : 14.084 158.934 2221 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.31 (0.23), residues: 1337 helix: -1.18 (0.52), residues: 106 sheet: -2.56 (0.41), residues: 185 loop : -1.47 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 274 HIS 0.003 0.001 HIS A 666 PHE 0.013 0.001 PHE B 460 TYR 0.014 0.001 TYR A 469 ARG 0.003 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 27 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7194 (p90) REVERT: A 512 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 484 GLN cc_start: 0.7804 (tt0) cc_final: 0.7309 (tm-30) outliers start: 29 outliers final: 20 residues processed: 54 average time/residue: 0.1689 time to fit residues: 16.1449 Evaluate side-chains 46 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 24 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 697 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11895 Z= 0.276 Angle : 0.547 7.812 16299 Z= 0.279 Chirality : 0.041 0.153 1994 Planarity : 0.004 0.043 1922 Dihedral : 14.390 160.328 2221 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.31 % Allowed : 16.79 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.25 (0.24), residues: 1337 helix: -1.04 (0.53), residues: 106 sheet: -2.72 (0.37), residues: 213 loop : -1.34 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 547 HIS 0.003 0.001 HIS A 666 PHE 0.011 0.001 PHE B 460 TYR 0.014 0.001 TYR A 469 ARG 0.002 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 24 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6799 (p90) REVERT: A 512 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8574 (tt) REVERT: B 447 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8785 (tmmt) REVERT: B 484 GLN cc_start: 0.7848 (tt0) cc_final: 0.7210 (tm-30) REVERT: B 643 MET cc_start: 0.7907 (ttm) cc_final: 0.7699 (mtp) outliers start: 29 outliers final: 20 residues processed: 50 average time/residue: 0.1662 time to fit residues: 14.8121 Evaluate side-chains 46 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 23 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 697 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11895 Z= 0.152 Angle : 0.489 8.350 16299 Z= 0.249 Chirality : 0.039 0.161 1994 Planarity : 0.003 0.042 1922 Dihedral : 14.181 164.571 2221 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.07 % Allowed : 17.26 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.06 (0.24), residues: 1337 helix: -0.97 (0.54), residues: 106 sheet: -2.48 (0.39), residues: 205 loop : -1.23 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 547 HIS 0.002 0.000 HIS A 109 PHE 0.006 0.001 PHE B 460 TYR 0.013 0.001 TYR B 469 ARG 0.002 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 27 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6490 (p90) REVERT: A 512 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (tt) REVERT: B 484 GLN cc_start: 0.7807 (tt0) cc_final: 0.7125 (tm-30) REVERT: B 643 MET cc_start: 0.7857 (ttm) cc_final: 0.7579 (mtp) outliers start: 26 outliers final: 16 residues processed: 52 average time/residue: 0.1739 time to fit residues: 15.9437 Evaluate side-chains 42 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 24 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 697 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11895 Z= 0.123 Angle : 0.490 9.477 16299 Z= 0.242 Chirality : 0.038 0.172 1994 Planarity : 0.003 0.042 1922 Dihedral : 13.824 166.993 2221 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.59 % Allowed : 17.82 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.85 (0.24), residues: 1337 helix: -0.60 (0.57), residues: 100 sheet: -2.37 (0.39), residues: 204 loop : -1.10 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 547 HIS 0.002 0.000 HIS A 109 PHE 0.006 0.001 PHE A 687 TYR 0.013 0.001 TYR B 469 ARG 0.003 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 24 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6142 (p90) REVERT: B 484 GLN cc_start: 0.7753 (tt0) cc_final: 0.7190 (tm-30) REVERT: B 643 MET cc_start: 0.7874 (ttm) cc_final: 0.7627 (mtp) outliers start: 20 outliers final: 14 residues processed: 43 average time/residue: 0.1700 time to fit residues: 13.5131 Evaluate side-chains 36 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 21 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 697 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 11895 Z= 0.370 Angle : 0.617 9.061 16299 Z= 0.309 Chirality : 0.043 0.179 1994 Planarity : 0.004 0.041 1922 Dihedral : 14.232 161.658 2221 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 1.59 % Allowed : 17.90 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.11 (0.24), residues: 1337 helix: -0.95 (0.53), residues: 112 sheet: -2.55 (0.41), residues: 186 loop : -1.31 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.003 0.001 HIS A 540 PHE 0.017 0.001 PHE B 460 TYR 0.014 0.002 TYR A 469 ARG 0.003 0.000 ARG B 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 22 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 75 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6322 (p90) REVERT: B 484 GLN cc_start: 0.8064 (tt0) cc_final: 0.7320 (tm-30) outliers start: 20 outliers final: 14 residues processed: 41 average time/residue: 0.1665 time to fit residues: 12.9178 Evaluate side-chains 37 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 22 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 697 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.074354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061578 restraints weight = 41786.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.063166 restraints weight = 21655.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.064216 restraints weight = 13831.685| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11895 Z= 0.121 Angle : 0.510 11.078 16299 Z= 0.248 Chirality : 0.038 0.170 1994 Planarity : 0.003 0.042 1922 Dihedral : 13.929 166.436 2221 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.51 % Allowed : 17.90 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.93 (0.24), residues: 1337 helix: -0.78 (0.54), residues: 106 sheet: -2.48 (0.39), residues: 206 loop : -1.12 (0.21), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 547 HIS 0.002 0.000 HIS A 109 PHE 0.006 0.001 PHE A 687 TYR 0.013 0.001 TYR A 469 ARG 0.002 0.000 ARG B 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.59 seconds wall clock time: 38 minutes 14.63 seconds (2294.63 seconds total)