Starting phenix.real_space_refine on Fri Sep 11 22:58:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_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/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.cif" model { file = "/net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da7_30624/09_2026/7da7_30624.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: {' U%rna3p_pyr:plan': 19, ' G%rna3p_pur:plan': 23, ' G%rna3p_pur:plan2': 23, ' A%rna3p_pur:plan': 19, ' A%rna3p_pur:plan2': 19, ' C%rna3p_pyr:plan': 28, ' C%rna3p_pyr:plan2': 28, ' U:plan': 1} Unresolved non-hydrogen planarities: 965 Time building chain proxies: 2.43, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 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: 0.97 Conformation dependent library (CDL) restraints added in 486.7 milliseconds 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: 1.03 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: 1.80 Time building geometry restraints manager: 1.29 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=" O3' G C 18 " pdb=" P U C 19 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.20e-02 6.94e+03 2.59e+01 bond pdb=" O3' U C 29 " pdb=" P A C 30 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.20e-02 6.94e+03 2.32e+01 bond pdb=" O3' C C 242 " pdb=" P A C 243 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.24e+01 bond pdb=" O3' A C 34 " pdb=" P C C 35 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.20e-02 6.94e+03 2.20e+01 bond pdb=" O3' G C 10 " pdb=" P A C 11 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.20e-02 6.94e+03 2.19e+01 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 15899 2.27 - 4.54: 691 4.54 - 6.81: 69 6.81 - 9.09: 18 9.09 - 11.36: 2 Bond angle restraints: 16679 Sorted by residual: 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=" O3' G C 13 " pdb=" C3' G C 13 " pdb=" C2' G C 13 " ideal model delta sigma weight residual 113.80 125.16 -11.36 2.00e+00 2.50e-01 3.22e+01 angle pdb=" C4' G C 45 " pdb=" C3' G C 45 " pdb=" O3' G C 45 " ideal model delta sigma weight residual 112.50 122.59 -10.09 2.00e+00 2.50e-01 2.55e+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=" N VAL A 582 " pdb=" CA VAL A 582 " pdb=" C VAL A 582 " ideal model delta sigma weight residual 112.29 107.75 4.54 9.40e-01 1.13e+00 2.33e+01 ... (remaining 16674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 7324 33.93 - 67.86: 293 67.86 - 101.79: 21 101.79 - 135.72: 0 135.72 - 169.64: 2 Dihedral angle restraints: 7640 sinusoidal: 3700 harmonic: 3940 Sorted by residual: 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 36.35 -40.93 77.27 1 3.10e+00 1.04e-01 7.79e+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 -35.15 38.01 -73.15 1 4.00e+00 6.25e-02 4.26e+02 dihedral pdb=" O4' U C 259 " pdb=" C2' U C 259 " pdb=" C1' U C 259 " pdb=" C3' U C 259 " ideal model delta sinusoidal sigma weight residual 25.59 -30.07 55.67 3 3.80e+00 6.93e-02 1.46e+02 ... (remaining 7637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 1917 0.181 - 0.362: 163 0.362 - 0.544: 2 0.544 - 0.725: 0 0.725 - 0.906: 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 -2.50 -1.59 -0.91 2.00e-01 2.50e+01 2.05e+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 -2.79 -2.40 -0.39 2.00e-01 2.50e+01 3.81e+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 3.120 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 3.040 nonbonded pdb=" OD1 ASN B 374 " pdb=" OG1 THR B 377 " model vdw 2.198 3.040 nonbonded pdb=" O ASN B 110 " pdb=" ND2 ASN B 134 " model vdw 2.222 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 3.830 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.008 0.379 12144 Z= 0.427 Angle : 1.148 47.090 16695 Z= 0.598 Chirality : 0.086 0.906 2083 Planarity : 0.005 0.049 1908 Dihedral : 16.506 169.644 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 % Allowed : 5.36 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 490 TYR 0.015 0.002 TYR B 384 PHE 0.017 0.001 PHE B 687 TRP 0.031 0.002 TRP B 274 HIS 0.005 0.001 HIS B 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.38 (12136) covalent geometry : angle 1.01765 / 0.54 (16679) SS BOND : bond 0.15131 / 5.58 ( 8) SS BOND : angle 17.19117 / 9.66 ( 16) hydrogen bonds : bond 0.28454 / 19.47 ( 112) hydrogen bonds : angle 9.92393 / 6.83 ( 273) *********************** 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 to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7802 (mmm) cc_final: 0.7180 (tpp) REVERT: A 208 ASN cc_start: 0.8118 (m-40) cc_final: 0.7872 (m110) REVERT: A 460 PHE cc_start: 0.7221 (t80) cc_final: 0.6909 (t80) REVERT: A 557 ASN cc_start: 0.8682 (t0) cc_final: 0.8396 (t0) REVERT: B 178 LEU cc_start: 0.8047 (mp) cc_final: 0.7726 (tt) REVERT: B 679 ASN cc_start: 0.7986 (m-40) cc_final: 0.7662 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1292 time to fit residues: 22.2052 Evaluate side-chains 48 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 62 ASN A 97 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 137 HIS A 142 ASN A 146 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 B 61 HIS B 62 ASN B 71 ASN B 97 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 142 ASN B 146 ASN B 158 ASN B 419 HIS B 451 GLN B 467 ASN B 471 GLN ** 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.106473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077022 restraints weight = 27543.249| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.00 r_work: 0.3211 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12144 Z= 0.131 Angle : 0.692 10.263 16695 Z= 0.333 Chirality : 0.046 0.216 2083 Planarity : 0.005 0.046 1908 Dihedral : 11.735 169.675 2398 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.20 % Allowed : 10.64 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.21), residues: 1330 helix: -2.58 (0.48), residues: 66 sheet: -2.99 (0.32), residues: 240 loop : -1.98 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 32 TYR 0.010 0.001 TYR B 684 PHE 0.018 0.001 PHE A 122 TRP 0.010 0.001 TRP B 244 HIS 0.009 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12136) covalent geometry : angle 0.69084 / 0.33 (16679) SS BOND : bond 0.00694 / 0.30 ( 8) SS BOND : angle 1.46799 / 0.88 ( 16) hydrogen bonds : bond 0.05292 / 3.71 ( 112) hydrogen bonds : angle 7.61789 / 5.11 ( 273) *********************** 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 81 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7961 (m-80) cc_final: 0.7029 (t80) REVERT: A 128 GLU cc_start: 0.8017 (tt0) cc_final: 0.7239 (tm-30) REVERT: A 153 LEU cc_start: 0.8266 (tt) cc_final: 0.8032 (tp) REVERT: A 331 LYS cc_start: 0.8889 (tttt) cc_final: 0.8668 (ttpp) REVERT: A 445 GLU cc_start: 0.8419 (tt0) cc_final: 0.7970 (pp20) REVERT: A 460 PHE cc_start: 0.7725 (t80) cc_final: 0.7096 (t80) REVERT: A 557 ASN cc_start: 0.8725 (t0) cc_final: 0.8461 (t0) REVERT: B 178 LEU cc_start: 0.8153 (mp) cc_final: 0.7673 (tt) REVERT: B 447 LYS cc_start: 0.8568 (tttp) cc_final: 0.8275 (tttp) REVERT: B 460 PHE cc_start: 0.6645 (t80) cc_final: 0.6239 (m-80) REVERT: B 637 ASN cc_start: 0.8486 (t0) cc_final: 0.8175 (t0) REVERT: B 679 ASN cc_start: 0.8295 (m-40) cc_final: 0.7672 (t0) outliers start: 15 outliers final: 3 residues processed: 81 average time/residue: 0.0953 time to fit residues: 12.0140 Evaluate side-chains 53 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 404 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.0570 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 77 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN B 63 GLN B 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.102269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072975 restraints weight = 28437.037| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.99 r_work: 0.3120 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12144 Z= 0.250 Angle : 0.716 9.422 16695 Z= 0.348 Chirality : 0.048 0.289 2083 Planarity : 0.005 0.048 1908 Dihedral : 10.842 163.548 2398 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.00 % Allowed : 13.36 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.22), residues: 1330 helix: -0.59 (0.77), residues: 42 sheet: -3.00 (0.32), residues: 240 loop : -1.79 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.014 0.002 TYR A 327 PHE 0.016 0.002 PHE B 635 TRP 0.016 0.001 TRP B 244 HIS 0.006 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (12136) covalent geometry : angle 0.71520 / 0.35 (16679) SS BOND : bond 0.00851 / 0.33 ( 8) SS BOND : angle 1.41025 / 0.74 ( 16) hydrogen bonds : bond 0.05980 / 4.22 ( 112) hydrogen bonds : angle 7.22788 / 4.85 ( 273) *********************** 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 77 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8009 (m-80) cc_final: 0.7143 (t80) REVERT: A 128 GLU cc_start: 0.8117 (tt0) cc_final: 0.7381 (tm-30) REVERT: A 460 PHE cc_start: 0.7732 (t80) cc_final: 0.7066 (t80) REVERT: B 152 LYS cc_start: 0.8205 (mppt) cc_final: 0.7861 (mppt) REVERT: B 158 ASN cc_start: 0.8471 (m-40) cc_final: 0.7912 (t0) REVERT: B 178 LEU cc_start: 0.8182 (mp) cc_final: 0.7659 (tt) REVERT: B 460 PHE cc_start: 0.6803 (t80) cc_final: 0.6596 (m-80) REVERT: B 461 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: B 511 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 637 ASN cc_start: 0.8671 (t0) cc_final: 0.8299 (t0) REVERT: B 679 ASN cc_start: 0.8427 (m-40) cc_final: 0.7861 (t0) outliers start: 25 outliers final: 11 residues processed: 75 average time/residue: 0.0939 time to fit residues: 11.0063 Evaluate side-chains 58 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN B 71 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.104443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075139 restraints weight = 28081.756| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.01 r_work: 0.3171 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12144 Z= 0.111 Angle : 0.590 8.843 16695 Z= 0.285 Chirality : 0.044 0.272 2083 Planarity : 0.004 0.045 1908 Dihedral : 10.268 163.338 2398 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.36 % Allowed : 15.52 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.23), residues: 1330 helix: -0.66 (0.75), residues: 54 sheet: -2.82 (0.33), residues: 242 loop : -1.38 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 32 TYR 0.007 0.001 TYR B 75 PHE 0.013 0.001 PHE A 122 TRP 0.008 0.001 TRP B 244 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (12136) covalent geometry : angle 0.58924 / 0.28 (16679) SS BOND : bond 0.00222 / 0.10 ( 8) SS BOND : angle 0.86702 / 0.47 ( 16) hydrogen bonds : bond 0.04191 / 2.95 ( 112) hydrogen bonds : angle 6.63706 / 4.45 ( 273) *********************** 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 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8071 (tt0) cc_final: 0.7596 (tm-30) REVERT: A 460 PHE cc_start: 0.7694 (t80) cc_final: 0.7021 (t80) REVERT: A 557 ASN cc_start: 0.8705 (t0) cc_final: 0.8461 (t0) REVERT: B 152 LYS cc_start: 0.8347 (mppt) cc_final: 0.7831 (mppt) REVERT: B 158 ASN cc_start: 0.8212 (m-40) cc_final: 0.7818 (t0) REVERT: B 211 LYS cc_start: 0.9340 (tppt) cc_final: 0.8190 (mtmt) REVERT: B 447 LYS cc_start: 0.8720 (tttp) cc_final: 0.8462 (tttp) REVERT: B 460 PHE cc_start: 0.6877 (t80) cc_final: 0.6395 (m-80) REVERT: B 637 ASN cc_start: 0.8637 (t0) cc_final: 0.8248 (t0) REVERT: B 679 ASN cc_start: 0.8458 (m-40) cc_final: 0.7789 (t0) outliers start: 17 outliers final: 8 residues processed: 70 average time/residue: 0.1054 time to fit residues: 11.4812 Evaluate side-chains 54 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN B 71 ASN B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.101474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072413 restraints weight = 28224.191| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.00 r_work: 0.3114 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12144 Z= 0.214 Angle : 0.667 11.919 16695 Z= 0.321 Chirality : 0.047 0.285 2083 Planarity : 0.004 0.043 1908 Dihedral : 10.099 161.360 2398 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.52 % Allowed : 15.92 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.23), residues: 1330 helix: -1.47 (0.68), residues: 56 sheet: -2.71 (0.34), residues: 232 loop : -1.46 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 490 TYR 0.013 0.001 TYR A 327 PHE 0.013 0.001 PHE A 635 TRP 0.011 0.001 TRP B 244 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (12136) covalent geometry : angle 0.66719 / 0.32 (16679) SS BOND : bond 0.00492 / 0.27 ( 8) SS BOND : angle 0.93100 / 0.51 ( 16) hydrogen bonds : bond 0.05169 / 3.59 ( 112) hydrogen bonds : angle 6.70090 / 4.51 ( 273) *********************** 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 66 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8163 (tt0) cc_final: 0.7650 (tm-30) REVERT: A 460 PHE cc_start: 0.7703 (t80) cc_final: 0.7018 (t80) REVERT: A 557 ASN cc_start: 0.8779 (t0) cc_final: 0.8518 (t0) REVERT: B 152 LYS cc_start: 0.8329 (mppt) cc_final: 0.7804 (mppt) REVERT: B 178 LEU cc_start: 0.8093 (mp) cc_final: 0.7484 (tt) REVERT: B 461 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: B 511 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 637 ASN cc_start: 0.8788 (t0) cc_final: 0.8384 (t0) REVERT: B 679 ASN cc_start: 0.8502 (m-40) cc_final: 0.7843 (t0) outliers start: 19 outliers final: 10 residues processed: 63 average time/residue: 0.0919 time to fit residues: 9.3592 Evaluate side-chains 54 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 33 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.102104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.073104 restraints weight = 28262.160| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.99 r_work: 0.3131 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12144 Z= 0.162 Angle : 0.610 10.980 16695 Z= 0.293 Chirality : 0.045 0.267 2083 Planarity : 0.004 0.042 1908 Dihedral : 9.941 161.752 2398 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.76 % Allowed : 16.96 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.23), residues: 1330 helix: -1.22 (0.71), residues: 56 sheet: -2.67 (0.33), residues: 232 loop : -1.34 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 435 TYR 0.008 0.001 TYR B 284 PHE 0.011 0.001 PHE A 122 TRP 0.007 0.001 TRP B 244 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (12136) covalent geometry : angle 0.60952 / 0.29 (16679) SS BOND : bond 0.00368 / 0.19 ( 8) SS BOND : angle 0.91258 / 0.51 ( 16) hydrogen bonds : bond 0.04461 / 3.11 ( 112) hydrogen bonds : angle 6.47252 / 4.36 ( 273) *********************** 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 69 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8114 (tt0) cc_final: 0.7666 (tm-30) REVERT: A 246 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8635 (tt) REVERT: A 445 GLU cc_start: 0.8500 (tt0) cc_final: 0.8111 (pp20) REVERT: A 460 PHE cc_start: 0.7615 (t80) cc_final: 0.6982 (t80) REVERT: A 557 ASN cc_start: 0.8764 (t0) cc_final: 0.8544 (t0) REVERT: B 152 LYS cc_start: 0.8363 (mppt) cc_final: 0.7769 (mppt) REVERT: B 176 GLU cc_start: 0.8000 (tt0) cc_final: 0.7760 (mp0) REVERT: B 178 LEU cc_start: 0.8073 (mp) cc_final: 0.7801 (mp) REVERT: B 447 LYS cc_start: 0.8693 (tttp) cc_final: 0.8366 (tptt) REVERT: B 511 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 637 ASN cc_start: 0.8822 (t0) cc_final: 0.8415 (t0) REVERT: B 679 ASN cc_start: 0.8536 (m-40) cc_final: 0.7880 (t0) outliers start: 22 outliers final: 15 residues processed: 68 average time/residue: 0.0850 time to fit residues: 9.6000 Evaluate side-chains 62 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 6 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.070410 restraints weight = 28867.326| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.02 r_work: 0.3062 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 12144 Z= 0.357 Angle : 0.777 9.843 16695 Z= 0.376 Chirality : 0.050 0.289 2083 Planarity : 0.005 0.042 1908 Dihedral : 10.210 160.084 2398 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 2.16 % Allowed : 16.80 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.23), residues: 1330 helix: -1.62 (0.69), residues: 56 sheet: -2.77 (0.34), residues: 230 loop : -1.57 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 313 TYR 0.014 0.002 TYR B 284 PHE 0.020 0.002 PHE B 631 TRP 0.011 0.002 TRP B 244 HIS 0.007 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.36 (12136) covalent geometry : angle 0.77685 / 0.38 (16679) SS BOND : bond 0.00688 / 0.31 ( 8) SS BOND : angle 1.15711 / 0.62 ( 16) hydrogen bonds : bond 0.05947 / 4.15 ( 112) hydrogen bonds : angle 6.96523 / 4.72 ( 273) *********************** 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 74 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8225 (tt0) cc_final: 0.7738 (tm-30) REVERT: A 460 PHE cc_start: 0.7662 (t80) cc_final: 0.6933 (t80) REVERT: B 134 ASN cc_start: 0.5733 (OUTLIER) cc_final: 0.5087 (m110) REVERT: B 176 GLU cc_start: 0.7963 (tt0) cc_final: 0.7700 (mp0) REVERT: B 178 LEU cc_start: 0.8024 (mp) cc_final: 0.7768 (mp) REVERT: B 511 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 637 ASN cc_start: 0.8927 (t0) cc_final: 0.8582 (t0) outliers start: 27 outliers final: 20 residues processed: 73 average time/residue: 0.0783 time to fit residues: 9.4886 Evaluate side-chains 67 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.101243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.072609 restraints weight = 28451.005| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.02 r_work: 0.3111 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12144 Z= 0.169 Angle : 0.645 10.746 16695 Z= 0.308 Chirality : 0.046 0.273 2083 Planarity : 0.004 0.041 1908 Dihedral : 9.987 161.562 2398 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.24 % Allowed : 16.80 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.23), residues: 1330 helix: -1.24 (0.71), residues: 56 sheet: -2.72 (0.34), residues: 232 loop : -1.40 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.008 0.001 TYR A 327 PHE 0.010 0.001 PHE B 122 TRP 0.007 0.001 TRP B 244 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (12136) covalent geometry : angle 0.64290 / 0.31 (16679) SS BOND : bond 0.00366 / 0.18 ( 8) SS BOND : angle 1.67606 / 0.95 ( 16) hydrogen bonds : bond 0.04722 / 3.28 ( 112) hydrogen bonds : angle 6.62456 / 4.47 ( 273) *********************** 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 75 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8189 (tt0) cc_final: 0.7757 (tm-30) REVERT: A 445 GLU cc_start: 0.8457 (tt0) cc_final: 0.8137 (pp20) REVERT: A 460 PHE cc_start: 0.7673 (t80) cc_final: 0.6998 (t80) REVERT: A 557 ASN cc_start: 0.8798 (t0) cc_final: 0.8550 (t0) REVERT: B 134 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5160 (m110) REVERT: B 176 GLU cc_start: 0.7971 (tt0) cc_final: 0.7729 (mp0) REVERT: B 178 LEU cc_start: 0.8057 (mp) cc_final: 0.7788 (mp) REVERT: B 447 LYS cc_start: 0.8681 (tttp) cc_final: 0.8287 (tptt) REVERT: B 511 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 637 ASN cc_start: 0.8827 (t0) cc_final: 0.8436 (t0) outliers start: 28 outliers final: 21 residues processed: 73 average time/residue: 0.0769 time to fit residues: 9.5507 Evaluate side-chains 71 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.101502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072933 restraints weight = 28237.231| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.99 r_work: 0.3123 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12144 Z= 0.135 Angle : 0.609 10.154 16695 Z= 0.290 Chirality : 0.045 0.255 2083 Planarity : 0.004 0.040 1908 Dihedral : 9.811 161.551 2398 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.68 % Allowed : 17.36 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.24), residues: 1330 helix: -0.90 (0.73), residues: 56 sheet: -2.66 (0.34), residues: 232 loop : -1.29 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.006 0.001 TYR A 327 PHE 0.011 0.001 PHE A 122 TRP 0.006 0.001 TRP B 244 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12136) covalent geometry : angle 0.60830 / 0.29 (16679) SS BOND : bond 0.00312 / 0.16 ( 8) SS BOND : angle 1.29199 / 0.73 ( 16) hydrogen bonds : bond 0.04126 / 2.88 ( 112) hydrogen bonds : angle 6.40472 / 4.30 ( 273) *********************** 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 72 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8134 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 445 GLU cc_start: 0.8518 (tt0) cc_final: 0.8144 (pp20) REVERT: A 460 PHE cc_start: 0.7644 (t80) cc_final: 0.6958 (t80) REVERT: A 557 ASN cc_start: 0.8753 (t0) cc_final: 0.8541 (t0) REVERT: B 107 LEU cc_start: 0.9044 (tp) cc_final: 0.8712 (tt) REVERT: B 134 ASN cc_start: 0.5728 (OUTLIER) cc_final: 0.4108 (m110) REVERT: B 211 LYS cc_start: 0.9364 (tppt) cc_final: 0.8147 (mtmt) REVERT: B 511 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 637 ASN cc_start: 0.8827 (t0) cc_final: 0.8462 (t0) outliers start: 21 outliers final: 16 residues processed: 71 average time/residue: 0.0775 time to fit residues: 9.2724 Evaluate side-chains 65 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 131 optimal weight: 0.0270 chunk 128 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074119 restraints weight = 28459.855| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.03 r_work: 0.3149 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12144 Z= 0.100 Angle : 0.585 10.061 16695 Z= 0.275 Chirality : 0.044 0.234 2083 Planarity : 0.004 0.040 1908 Dihedral : 9.617 161.420 2398 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.60 % Allowed : 17.52 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.24), residues: 1330 helix: -0.59 (0.75), residues: 56 sheet: -2.35 (0.36), residues: 206 loop : -1.31 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.005 0.001 TYR B 303 PHE 0.011 0.001 PHE B 122 TRP 0.006 0.001 TRP A 657 HIS 0.002 0.000 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (12136) covalent geometry : angle 0.58439 / 0.27 (16679) SS BOND : bond 0.00209 / 0.11 ( 8) SS BOND : angle 1.07868 / 0.61 ( 16) hydrogen bonds : bond 0.03565 / 2.46 ( 112) hydrogen bonds : angle 6.12385 / 4.12 ( 273) ********************** 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 75 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8103 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 208 ASN cc_start: 0.8744 (m-40) cc_final: 0.8488 (m110) REVERT: A 364 ASP cc_start: 0.8189 (m-30) cc_final: 0.7965 (m-30) REVERT: A 445 GLU cc_start: 0.8492 (tt0) cc_final: 0.8119 (pp20) REVERT: A 460 PHE cc_start: 0.7687 (t80) cc_final: 0.7008 (t80) REVERT: B 107 LEU cc_start: 0.9005 (tp) cc_final: 0.8680 (tt) REVERT: B 134 ASN cc_start: 0.5712 (OUTLIER) cc_final: 0.4078 (m110) REVERT: B 211 LYS cc_start: 0.9344 (tppt) cc_final: 0.8090 (mtmt) REVERT: B 364 ASP cc_start: 0.7968 (m-30) cc_final: 0.7462 (m-30) REVERT: B 447 LYS cc_start: 0.8515 (tttp) cc_final: 0.8147 (tptp) REVERT: B 511 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 637 ASN cc_start: 0.8779 (t0) cc_final: 0.8498 (t0) outliers start: 20 outliers final: 12 residues processed: 73 average time/residue: 0.0976 time to fit residues: 11.1418 Evaluate side-chains 66 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 0.0060 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.102486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073893 restraints weight = 28356.542| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.02 r_work: 0.3145 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12144 Z= 0.110 Angle : 0.584 9.634 16695 Z= 0.275 Chirality : 0.044 0.200 2083 Planarity : 0.004 0.040 1908 Dihedral : 9.500 160.680 2398 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.28 % Allowed : 18.08 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.24), residues: 1330 helix: -1.13 (0.68), residues: 68 sheet: -2.51 (0.34), residues: 232 loop : -1.14 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.006 0.001 TYR B 303 PHE 0.010 0.001 PHE A 122 TRP 0.006 0.001 TRP A 657 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (12136) covalent geometry : angle 0.58354 / 0.27 (16679) SS BOND : bond 0.00217 / 0.11 ( 8) SS BOND : angle 1.04286 / 0.58 ( 16) hydrogen bonds : bond 0.03710 / 2.57 ( 112) hydrogen bonds : angle 6.09060 / 4.10 ( 273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.82 seconds wall clock time: 45 minutes 41.23 seconds (2741.23 seconds total)