Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 07:28:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da7_30624/04_2023/7da7_30624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da7_30624/04_2023/7da7_30624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da7_30624/04_2023/7da7_30624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da7_30624/04_2023/7da7_30624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da7_30624/04_2023/7da7_30624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da7_30624/04_2023/7da7_30624.pdb" } resolution = 3.47 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= 0.003 sd= 0.041 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 90 5.49 5 S 28 5.16 5 C 7309 2.51 5 N 1838 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 571": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11825 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5372 Classifications: {'peptide': 669} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 640} Chain breaks: 1 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5372 Classifications: {'peptide': 669} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 640} Chain breaks: 1 Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1081 Classifications: {'RNA': 90} Modifications used: {'rna3p_pur': 42, 'rna3p_pyr': 47} Link IDs: {'rna3p': 89} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 959 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {' G%rna3p_pur:plan2': 23, ' C%rna3p_pyr:plan': 28, ' A%rna3p_pur:plan2': 19, ' U%rna3p_pyr:plan': 19, ' U:plan': 1, ' C%rna3p_pyr:plan2': 28, ' G%rna3p_pur:plan': 23, ' A%rna3p_pur:plan': 19} Unresolved non-hydrogen planarities: 965 Time building chain proxies: 6.67, per 1000 atoms: 0.56 Number of scatterers: 11825 At special positions: 0 Unit cell: (104.14, 96.76, 166.46, 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 90 15.00 O 2560 8.00 N 1838 7.00 C 7309 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=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 123 " distance=1.84 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 678 " distance=2.02 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=1.65 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 678 " distance=2.00 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 18 sheets defined 12.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.408A pdb=" N CYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.483A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.031A pdb=" N THR A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.483A pdb=" N GLY A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.119A pdb=" N PHE A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.908A pdb=" N VAL A 403 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 404 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.537A pdb=" N TRP A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.206A pdb=" N TRP A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.953A 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 664 removed outlier: 3.674A pdb=" N SER A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TRP A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 5.181A 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 93 through 98 Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.341A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.631A pdb=" N TRP B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.525A pdb=" N GLY B 271 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 3.685A pdb=" N VAL B 403 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 404 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS B 407 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.549A pdb=" N TRP B 453 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 4.289A pdb=" N TRP B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.647A 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 664 removed outlier: 3.562A pdb=" N SER B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TRP B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.514A pdb=" N PHE B 692 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.068A pdb=" N ALA A 36 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 57 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 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 253 through 255 removed outlier: 7.084A pdb=" N LEU A 254 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 304 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 328 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 361 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU A 385 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 413 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 487 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.611A pdb=" N LEU A 314 " --> pdb=" O ASN A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.649A pdb=" N GLN A 446 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 470 " --> pdb=" O LYS A 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.231A pdb=" N ALA B 36 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 57 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 129 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 255 removed outlier: 7.080A pdb=" N LEU B 254 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 304 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 328 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 361 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 385 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 413 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 487 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.616A pdb=" N LEU B 314 " --> pdb=" O ASN B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AB8, first strand: chain 'B' and resid 445 through 447 removed outlier: 6.577A pdb=" N GLN B 446 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 470 " --> pdb=" O LYS B 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 640 through 641 112 hydrogen bonds defined for protein. 273 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: 3.63 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1774 1.31 - 1.44: 3186 1.44 - 1.57: 6962 1.57 - 1.70: 178 1.70 - 1.83: 36 Bond restraints: 12136 Sorted by residual: bond pdb=" C GLU A 653 " pdb=" O GLU A 653 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.33e-02 5.65e+03 2.11e+01 bond pdb=" O3' G C 18 " pdb=" P U C 19 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.66e+01 bond pdb=" O3' U C 29 " pdb=" P A C 30 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" O3' C C 242 " pdb=" P A C 243 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.43e+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 1.41e+01 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 616 105.97 - 112.97: 6890 112.97 - 119.97: 4120 119.97 - 126.97: 4927 126.97 - 133.98: 126 Bond angle restraints: 16679 Sorted by residual: angle pdb=" O3' G C 13 " pdb=" C3' G C 13 " pdb=" C2' G C 13 " ideal model delta sigma weight residual 113.70 125.16 -11.46 1.50e+00 4.44e-01 5.83e+01 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 113.86 105.67 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" C4' G C 45 " pdb=" C3' G C 45 " pdb=" O3' G C 45 " ideal model delta sigma weight residual 113.00 122.59 -9.59 1.50e+00 4.44e-01 4.09e+01 angle pdb=" CA HIS A 237 " pdb=" C HIS A 237 " pdb=" O HIS A 237 " ideal model delta sigma weight residual 121.88 115.33 6.55 1.30e+00 5.92e-01 2.54e+01 angle pdb=" C4' A C 258 " pdb=" C3' A C 258 " pdb=" O3' A C 258 " ideal model delta sigma weight residual 113.00 120.48 -7.48 1.50e+00 4.44e-01 2.49e+01 ... (remaining 16674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 7335 33.93 - 67.86: 267 67.86 - 101.79: 36 101.79 - 135.72: 0 135.72 - 169.64: 2 Dihedral angle restraints: 7640 sinusoidal: 3700 harmonic: 3940 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 82.00 166.03 -84.03 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 -40.93 76.93 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 38.01 -73.01 1 8.00e+00 1.56e-02 1.06e+02 ... (remaining 7637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2027 0.177 - 0.354: 53 0.354 - 0.531: 2 0.531 - 0.708: 0 0.708 - 0.885: 1 Chirality restraints: 2083 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 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA PRO B 681 " pdb=" N PRO B 681 " pdb=" C PRO B 681 " pdb=" CB PRO B 681 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C2' G C 13 " pdb=" C3' G C 13 " pdb=" O2' G C 13 " pdb=" C1' G C 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2080 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 681 " -0.017 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PRO B 681 " 0.064 2.00e-02 2.50e+03 pdb=" O PRO B 681 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS B 682 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 593 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN B 593 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN B 593 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 594 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 626 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C VAL B 626 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 626 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 627 " 0.013 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 202 2.64 - 3.20: 11020 3.20 - 3.77: 16869 3.77 - 4.33: 24683 4.33 - 4.90: 39765 Nonbonded interactions: 92539 Sorted by model distance: nonbonded pdb=" O HIS B 683 " pdb=" ND1 HIS B 683 " model vdw 2.072 2.520 nonbonded pdb=" O ASN A 679 " pdb=" OD1 ASN A 679 " model vdw 2.166 3.040 nonbonded pdb=" O PHE A 85 " pdb=" O2' G C 14 " model vdw 2.197 2.440 nonbonded pdb=" OD1 ASN B 374 " pdb=" OG1 THR B 377 " model vdw 2.198 2.440 nonbonded pdb=" O ASN B 110 " pdb=" ND2 ASN B 134 " model vdw 2.222 2.520 ... (remaining 92534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 12.860 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.470 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.007 0.085 12136 Z= 0.472 Angle : 0.969 11.457 16679 Z= 0.581 Chirality : 0.071 0.885 2083 Planarity : 0.005 0.049 1908 Dihedral : 16.866 169.644 5044 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.23 % 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: -4.59 (0.19), residues: 1330 helix: -4.99 (0.17), residues: 66 sheet: -3.41 (0.32), residues: 208 loop : -3.12 (0.16), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3020 time to fit residues: 51.3877 Evaluate side-chains 43 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 62 ASN A 97 GLN A 109 HIS A 118 GLN A 137 HIS A 142 ASN A 157 HIS A 208 ASN A 451 GLN A 467 ASN A 471 GLN A 495 ASN A 518 ASN A 585 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 637 ASN A 646 ASN A 660 ASN B 61 HIS B 62 ASN B 63 GLN B 71 ASN B 97 GLN B 118 GLN B 142 ASN B 146 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 HIS B 446 GLN B 451 GLN B 467 ASN B 471 GLN B 518 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 646 ASN B 660 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12136 Z= 0.193 Angle : 0.609 10.076 16679 Z= 0.307 Chirality : 0.041 0.205 2083 Planarity : 0.004 0.047 1908 Dihedral : 14.506 173.981 2398 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.36 % 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: -3.18 (0.22), residues: 1330 helix: -2.52 (0.51), residues: 54 sheet: -2.99 (0.32), residues: 240 loop : -2.01 (0.18), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 75 average time/residue: 0.2392 time to fit residues: 28.2042 Evaluate side-chains 43 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1253 time to fit residues: 3.0915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 102 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 71 ASN A 77 GLN A 146 ASN A 446 GLN A 518 ASN B 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 12136 Z= 0.358 Angle : 0.665 10.240 16679 Z= 0.334 Chirality : 0.044 0.322 2083 Planarity : 0.005 0.051 1908 Dihedral : 13.852 171.181 2398 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer Outliers : 1.92 % 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: -2.81 (0.23), residues: 1330 helix: -0.63 (0.77), residues: 42 sheet: -2.94 (0.32), residues: 240 loop : -1.78 (0.19), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 71 average time/residue: 0.2143 time to fit residues: 24.1321 Evaluate side-chains 49 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1090 time to fit residues: 4.1074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 446 GLN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12136 Z= 0.149 Angle : 0.540 9.287 16679 Z= 0.268 Chirality : 0.039 0.181 2083 Planarity : 0.004 0.048 1908 Dihedral : 13.447 172.125 2398 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.04 % 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: -2.32 (0.23), residues: 1330 helix: 0.21 (0.86), residues: 42 sheet: -2.76 (0.33), residues: 240 loop : -1.40 (0.20), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.2205 time to fit residues: 21.6789 Evaluate side-chains 44 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1224 time to fit residues: 2.8194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS B 259 ASN B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12136 Z= 0.205 Angle : 0.552 11.869 16679 Z= 0.272 Chirality : 0.040 0.259 2083 Planarity : 0.004 0.044 1908 Dihedral : 13.135 170.879 2398 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.48 % 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: -2.19 (0.23), residues: 1330 helix: 0.08 (0.84), residues: 42 sheet: -2.55 (0.34), residues: 230 loop : -1.35 (0.20), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 1.386 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.2193 time to fit residues: 17.6787 Evaluate side-chains 41 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1163 time to fit residues: 2.4621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 136 optimal weight: 40.0000 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 259 ASN B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12136 Z= 0.222 Angle : 0.549 11.161 16679 Z= 0.274 Chirality : 0.040 0.140 2083 Planarity : 0.004 0.042 1908 Dihedral : 12.919 170.198 2398 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.88 % 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: -2.08 (0.24), residues: 1330 helix: -0.01 (0.85), residues: 42 sheet: -2.48 (0.34), residues: 230 loop : -1.26 (0.20), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.497 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.2208 time to fit residues: 17.6097 Evaluate side-chains 40 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1200 time to fit residues: 2.8803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 ASN B 367 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 12136 Z= 0.343 Angle : 0.617 9.992 16679 Z= 0.309 Chirality : 0.042 0.166 2083 Planarity : 0.004 0.041 1908 Dihedral : 13.100 170.007 2398 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 1.12 % 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 (0.24), residues: 1330 helix: -0.52 (0.82), residues: 42 sheet: -2.66 (0.33), residues: 232 loop : -1.34 (0.20), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 0.2095 time to fit residues: 18.7860 Evaluate side-chains 42 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1056 time to fit residues: 2.9268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 130 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 446 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12136 Z= 0.176 Angle : 0.543 9.378 16679 Z= 0.269 Chirality : 0.040 0.159 2083 Planarity : 0.004 0.041 1908 Dihedral : 12.980 169.704 2398 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.24 % 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: -2.01 (0.24), residues: 1330 helix: -0.05 (0.85), residues: 42 sheet: -2.48 (0.34), residues: 232 loop : -1.19 (0.20), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.2279 time to fit residues: 17.2977 Evaluate side-chains 41 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12136 Z= 0.278 Angle : 0.577 9.349 16679 Z= 0.289 Chirality : 0.041 0.168 2083 Planarity : 0.004 0.041 1908 Dihedral : 13.038 169.623 2398 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer Outliers : 0.32 % 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: -2.13 (0.24), residues: 1330 helix: -0.37 (0.83), residues: 42 sheet: -2.59 (0.33), residues: 232 loop : -1.26 (0.20), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 0.2229 time to fit residues: 16.0166 Evaluate side-chains 38 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1118 time to fit residues: 2.0574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 129 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12136 Z= 0.217 Angle : 0.552 12.791 16679 Z= 0.272 Chirality : 0.040 0.138 2083 Planarity : 0.004 0.040 1908 Dihedral : 12.946 169.225 2398 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: -2.05 (0.24), residues: 1330 helix: -0.16 (0.85), residues: 42 sheet: -2.56 (0.34), residues: 232 loop : -1.20 (0.20), residues: 1056 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2112 time to fit residues: 15.9102 Evaluate side-chains 40 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.0050 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.101107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072818 restraints weight = 28668.977| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.09 r_work: 0.3121 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12136 Z= 0.242 Angle : 0.563 11.456 16679 Z= 0.279 Chirality : 0.040 0.135 2083 Planarity : 0.004 0.040 1908 Dihedral : 12.920 169.023 2398 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % 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: -2.00 (0.24), residues: 1330 helix: -0.16 (0.85), residues: 42 sheet: -2.33 (0.36), residues: 212 loop : -1.24 (0.20), residues: 1076 =============================================================================== Job complete usr+sys time: 2212.92 seconds wall clock time: 41 minutes 24.55 seconds (2484.55 seconds total)