Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 06:44:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/07_2023/7das_30626.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/07_2023/7das_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_30626/07_2023/7das_30626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/07_2023/7das_30626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/07_2023/7das_30626.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7das_30626/07_2023/7das_30626.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 492 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: 6.14, per 1000 atoms: 0.53 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: 4.76 Conformation dependent library (CDL) restraints added in 1.6 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: 2.69 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: 3.29 Time building geometry restraints manager: 5.07 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: 7153 33.25 - 66.49: 222 66.49 - 99.74: 35 99.74 - 132.99: 0 132.99 - 166.23: 1 Dihedral angle restraints: 7411 sinusoidal: 3448 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 7408 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: 2.820 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: 12.570 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.150 Find NCS groups from input model: 0.690 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.220 ------------------------------------------------------------------------------- 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 : 16.280 166.233 4801 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 % 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 *********************** 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 outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3164 time to fit residues: 46.8083 Evaluate side-chains 39 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7889 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 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 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: 0.7781 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 11895 Z= 0.224 Angle : 0.574 10.206 16299 Z= 0.294 Chirality : 0.041 0.142 1994 Planarity : 0.004 0.037 1922 Dihedral : 12.670 178.520 2143 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 1.35 % 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: -1.01 (0.56), residues: 88 sheet: -2.53 (0.37), residues: 189 loop : -1.88 (0.19), residues: 1060 *********************** 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: 17 poor density : 41 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 52 average time/residue: 0.2350 time to fit residues: 19.2532 Evaluate side-chains 37 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1111 time to fit residues: 3.5218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 0.0270 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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** A 639 ASN B 63 GLN B 146 ASN ** 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: 0.7780 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 11895 Z= 0.149 Angle : 0.489 8.640 16299 Z= 0.253 Chirality : 0.039 0.144 1994 Planarity : 0.003 0.035 1922 Dihedral : 11.862 172.350 2143 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.56 % 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: -2.26 (0.23), residues: 1337 helix: -0.75 (0.59), residues: 88 sheet: -2.40 (0.38), residues: 194 loop : -1.49 (0.20), residues: 1055 *********************** 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 44 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 44 average time/residue: 0.1991 time to fit residues: 15.0282 Evaluate side-chains 23 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.0060 chunk 14 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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** B 63 GLN B 106 ASN B 109 HIS B 451 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 11895 Z= 0.332 Angle : 0.611 8.241 16299 Z= 0.314 Chirality : 0.043 0.182 1994 Planarity : 0.004 0.039 1922 Dihedral : 12.197 160.988 2143 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 1.27 % 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: -2.52 (0.23), residues: 1337 helix: -1.40 (0.51), residues: 106 sheet: -2.49 (0.40), residues: 183 loop : -1.67 (0.19), residues: 1048 *********************** 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 46 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 45 average time/residue: 0.2093 time to fit residues: 15.8708 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1393 time to fit residues: 3.6766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 610 GLN B 40 HIS B 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11895 Z= 0.277 Angle : 0.553 7.606 16299 Z= 0.284 Chirality : 0.041 0.163 1994 Planarity : 0.004 0.042 1922 Dihedral : 12.338 162.263 2143 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.80 % 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: -2.38 (0.23), residues: 1337 helix: -1.29 (0.52), residues: 106 sheet: -2.47 (0.41), residues: 185 loop : -1.55 (0.20), residues: 1046 *********************** 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 33 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 23 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 33 average time/residue: 0.1628 time to fit residues: 10.4474 Evaluate side-chains 27 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1003 time to fit residues: 2.8053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 5.9990 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: 3.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 11895 Z= 0.336 Angle : 0.595 7.251 16299 Z= 0.306 Chirality : 0.043 0.157 1994 Planarity : 0.004 0.045 1922 Dihedral : 12.633 156.685 2143 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer Outliers : 0.95 % 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: -2.44 (0.23), residues: 1337 helix: -1.40 (0.50), residues: 112 sheet: -2.69 (0.40), residues: 185 loop : -1.54 (0.20), residues: 1040 *********************** 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 33 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 21 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 33 average time/residue: 0.1971 time to fit residues: 11.7906 Evaluate side-chains 26 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1153 time to fit residues: 2.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 98 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11895 Z= 0.171 Angle : 0.498 7.697 16299 Z= 0.255 Chirality : 0.039 0.167 1994 Planarity : 0.003 0.044 1922 Dihedral : 12.378 162.442 2143 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 0.72 % 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: -2.24 (0.24), residues: 1337 helix: -1.25 (0.52), residues: 112 sheet: -2.66 (0.38), residues: 204 loop : -1.33 (0.20), residues: 1021 *********************** 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 33 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 24 time to evaluate : 1.350 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 32 average time/residue: 0.1781 time to fit residues: 10.8474 Evaluate side-chains 21 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 122 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4234 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= 0.149 Angle : 0.493 9.093 16299 Z= 0.249 Chirality : 0.039 0.142 1994 Planarity : 0.003 0.043 1922 Dihedral : 12.062 166.252 2143 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 0.16 % 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: -2.04 (0.24), residues: 1337 helix: -0.94 (0.54), residues: 106 sheet: -2.54 (0.37), residues: 217 loop : -1.18 (0.21), residues: 1014 *********************** 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 27 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 1.311 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 26 average time/residue: 0.1653 time to fit residues: 8.7787 Evaluate side-chains 22 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 0.0050 chunk 38 optimal weight: 0.0980 chunk 113 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 564 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4351 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= 0.126 Angle : 0.478 8.457 16299 Z= 0.241 Chirality : 0.038 0.168 1994 Planarity : 0.003 0.044 1922 Dihedral : 11.845 167.339 2143 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.56 % 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: -1.86 (0.24), residues: 1337 helix: -0.60 (0.57), residues: 100 sheet: -2.39 (0.38), residues: 215 loop : -1.08 (0.21), residues: 1022 *********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 1.351 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.1807 time to fit residues: 10.5865 Evaluate side-chains 22 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1090 time to fit residues: 2.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 539 GLN B 541 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 11895 Z= 0.408 Angle : 0.648 7.750 16299 Z= 0.329 Chirality : 0.044 0.175 1994 Planarity : 0.004 0.043 1922 Dihedral : 12.626 159.774 2143 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer Outliers : 0.40 % 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: -2.29 (0.24), residues: 1337 helix: -1.05 (0.52), residues: 112 sheet: -2.83 (0.37), residues: 210 loop : -1.35 (0.20), residues: 1015 ********************** 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 28 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 1.400 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 0.1821 time to fit residues: 9.5859 Evaluate side-chains 23 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1581 time to fit residues: 2.0431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.074549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061778 restraints weight = 41757.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063379 restraints weight = 21605.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064410 restraints weight = 13759.276| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4586 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= 0.118 Angle : 0.502 9.112 16299 Z= 0.251 Chirality : 0.038 0.156 1994 Planarity : 0.003 0.044 1922 Dihedral : 12.235 166.290 2143 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.08 % 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: -1.98 (0.24), residues: 1337 helix: -0.81 (0.54), residues: 106 sheet: -2.53 (0.37), residues: 217 loop : -1.14 (0.21), residues: 1014 =============================================================================== Job complete usr+sys time: 1816.50 seconds wall clock time: 34 minutes 21.36 seconds (2061.36 seconds total)