Starting phenix.real_space_refine on Sat Feb 7 19:44:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lm3_63214/02_2026/9lm3_63214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lm3_63214/02_2026/9lm3_63214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lm3_63214/02_2026/9lm3_63214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lm3_63214/02_2026/9lm3_63214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lm3_63214/02_2026/9lm3_63214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lm3_63214/02_2026/9lm3_63214.map" } resolution = 2.6 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= 0.002 sd= 0.149 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: 6 Type Number sf(0) Gaussians P 225 5.49 5 S 66 5.16 5 C 11162 2.51 5 N 3275 2.21 5 O 4125 1.98 5 H 16742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35595 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9512 Classifications: {'peptide': 583} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 563} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 9479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9479 Classifications: {'peptide': 580} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 9512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9512 Classifications: {'peptide': 583} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 563} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 399 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1805 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 25, 'rna3p_pyr': 16} Link IDs: {'rna2p': 16, 'rna3p': 40} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "F" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 399 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "G" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1805 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 37} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "J" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 399 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "M" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "N" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "O" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "K" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1805 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 27, 'rna3p_pyr': 14} Link IDs: {'rna2p': 16, 'rna3p': 40} Time building chain proxies: 6.20, per 1000 atoms: 0.17 Number of scatterers: 35595 At special positions: 0 Unit cell: (112.35, 142.31, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 225 15.00 O 4125 8.00 N 3275 7.00 C 11162 6.00 H 16742 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.81 Conformation dependent library (CDL) restraints added in 900.4 milliseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3302 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 25 sheets defined 52.6% alpha, 12.7% beta 63 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 63 through 88 removed outlier: 3.730A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.920A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 169 through 193 removed outlier: 4.700A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N MET A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.830A pdb=" N THR A 246 " --> pdb=" O ASP A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 269 through 286 Processing helix chain 'A' and resid 302 through 326 removed outlier: 3.809A pdb=" N VAL A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.805A pdb=" N LYS A 344 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 428 through 445 removed outlier: 4.472A pdb=" N LYS A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.742A pdb=" N MET A 489 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.506A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 524' Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 566 through 586 removed outlier: 3.544A pdb=" N PHE A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.151A pdb=" N LEU E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP E 8 " --> pdb=" O THR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 38 through 41 Processing helix chain 'E' and resid 63 through 87 removed outlier: 3.629A pdb=" N ASP E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 169 through 193 removed outlier: 4.648A pdb=" N ILE E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N MET E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 269 through 286 Processing helix chain 'E' and resid 302 through 328 removed outlier: 3.627A pdb=" N LEU E 306 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.528A pdb=" N LYS E 344 " --> pdb=" O HIS E 341 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS E 346 " --> pdb=" O PHE E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 364 Processing helix chain 'E' and resid 375 through 389 removed outlier: 4.333A pdb=" N ARG E 379 " --> pdb=" O GLY E 375 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 416 through 423 Processing helix chain 'E' and resid 428 through 445 removed outlier: 4.666A pdb=" N LYS E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASN E 441 " --> pdb=" O GLU E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 Processing helix chain 'E' and resid 484 through 488 Processing helix chain 'E' and resid 513 through 518 removed outlier: 3.645A pdb=" N PHE E 518 " --> pdb=" O MET E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 524 Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 556 through 560 removed outlier: 4.416A pdb=" N ARG E 559 " --> pdb=" O ASP E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 586 removed outlier: 3.642A pdb=" N PHE E 570 " --> pdb=" O PHE E 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 15 through 24 Processing helix chain 'I' and resid 26 through 35 Processing helix chain 'I' and resid 38 through 41 Processing helix chain 'I' and resid 62 through 87 removed outlier: 3.669A pdb=" N ILE I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 124 through 128 removed outlier: 3.635A pdb=" N SER I 127 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE I 128 " --> pdb=" O PHE I 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 124 through 128' Processing helix chain 'I' and resid 129 through 140 Processing helix chain 'I' and resid 146 through 158 Processing helix chain 'I' and resid 169 through 192 removed outlier: 4.698A pdb=" N ILE I 180 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N MET I 181 " --> pdb=" O ILE I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.753A pdb=" N THR I 246 " --> pdb=" O ASP I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 269 through 287 Processing helix chain 'I' and resid 308 through 328 removed outlier: 3.810A pdb=" N VAL I 316 " --> pdb=" O PHE I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 364 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 416 through 424 Processing helix chain 'I' and resid 428 through 445 removed outlier: 4.676A pdb=" N LYS I 440 " --> pdb=" O VAL I 436 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN I 441 " --> pdb=" O GLU I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 475 removed outlier: 3.616A pdb=" N ASN I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 489 removed outlier: 3.788A pdb=" N MET I 489 " --> pdb=" O MET I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 Processing helix chain 'I' and resid 519 through 523 Processing helix chain 'I' and resid 545 through 556 Processing helix chain 'I' and resid 566 through 586 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.629A pdb=" N GLU A 240 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 Processing sheet with id=AA5, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 292 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.118A pdb=" N VAL A 455 " --> pdb=" O TYR A 499 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 501 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET A 457 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 532 removed outlier: 6.718A pdb=" N LYS A 531 " --> pdb=" O TYR A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 49 Processing sheet with id=AB2, first strand: chain 'E' and resid 195 through 199 removed outlier: 4.536A pdb=" N GLU E 240 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 195 through 199 Processing sheet with id=AB4, first strand: chain 'E' and resid 217 through 219 Processing sheet with id=AB5, first strand: chain 'E' and resid 256 through 257 Processing sheet with id=AB6, first strand: chain 'E' and resid 291 through 292 Processing sheet with id=AB7, first strand: chain 'E' and resid 411 through 412 removed outlier: 6.226A pdb=" N VAL E 455 " --> pdb=" O TYR E 499 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL E 501 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET E 457 " --> pdb=" O VAL E 501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 397 through 399 Processing sheet with id=AB9, first strand: chain 'I' and resid 43 through 50 Processing sheet with id=AC1, first strand: chain 'I' and resid 195 through 199 removed outlier: 4.506A pdb=" N GLU I 240 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 195 through 199 Processing sheet with id=AC3, first strand: chain 'I' and resid 217 through 220 Processing sheet with id=AC4, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AC5, first strand: chain 'I' and resid 291 through 292 Processing sheet with id=AC6, first strand: chain 'I' and resid 411 through 412 removed outlier: 6.060A pdb=" N VAL I 455 " --> pdb=" O TYR I 499 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL I 501 " --> pdb=" O VAL I 455 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET I 457 " --> pdb=" O VAL I 501 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE I 500 " --> pdb=" O HIS I 493 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS I 493 " --> pdb=" O ILE I 500 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 397 through 398 734 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 159 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 8.92 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16709 1.03 - 1.23: 199 1.23 - 1.42: 8609 1.42 - 1.62: 10792 1.62 - 1.81: 99 Bond restraints: 36408 Sorted by residual: bond pdb=" CB GLU E 395 " pdb=" CG GLU E 395 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DA B 56 " pdb=" O3' DA B 56 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" N GLU E 395 " pdb=" H GLU E 395 " ideal model delta sigma weight residual 0.860 0.838 0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3' DT B 57 " pdb=" O3' DT B 57 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" C2' A G 14 " pdb=" C1' A G 14 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.50e-02 4.44e+03 1.03e+00 ... (remaining 36403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 63866 1.49 - 2.99: 1750 2.99 - 4.48: 136 4.48 - 5.98: 15 5.98 - 7.47: 5 Bond angle restraints: 65772 Sorted by residual: angle pdb=" CA GLU E 395 " pdb=" CB GLU E 395 " pdb=" CG GLU E 395 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" N TYR I 159 " pdb=" CA TYR I 159 " pdb=" C TYR I 159 " ideal model delta sigma weight residual 110.80 104.01 6.79 2.13e+00 2.20e-01 1.02e+01 angle pdb=" CB GLU E 395 " pdb=" CG GLU E 395 " pdb=" CD GLU E 395 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.70e+00 3.46e-01 9.42e+00 angle pdb=" C GLN A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.23e+00 angle pdb=" C3' C C 13 " pdb=" O3' C C 13 " pdb=" P A C 14 " ideal model delta sigma weight residual 120.20 124.14 -3.94 1.50e+00 4.44e-01 6.91e+00 ... (remaining 65767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 16058 35.13 - 70.26: 920 70.26 - 105.39: 65 105.39 - 140.53: 17 140.53 - 175.66: 21 Dihedral angle restraints: 17081 sinusoidal: 11052 harmonic: 6029 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 200.00 25.47 174.53 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U K 9 " pdb=" C1' U K 9 " pdb=" N1 U K 9 " pdb=" C2 U K 9 " ideal model delta sinusoidal sigma weight residual 200.00 31.87 168.13 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual -160.00 -2.06 -157.94 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 17078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2405 0.039 - 0.078: 598 0.078 - 0.117: 169 0.117 - 0.155: 49 0.155 - 0.194: 5 Chirality restraints: 3226 Sorted by residual: chirality pdb=" C1' G G 8 " pdb=" O4' G G 8 " pdb=" C2' G G 8 " pdb=" N9 G G 8 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" P A C 14 " pdb=" OP1 A C 14 " pdb=" OP2 A C 14 " pdb=" O5' A C 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.60 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" C1' G C 8 " pdb=" O4' G C 8 " pdb=" C2' G C 8 " pdb=" N9 G C 8 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 3223 not shown) Planarity restraints: 4516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 8 " 0.022 2.00e-02 2.50e+03 1.07e-02 3.70e+00 pdb=" N9 G C 8 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G C 8 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G C 8 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 8 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G C 8 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G C 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G C 8 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 8 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G C 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 8 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G C 8 " -0.000 2.00e-02 2.50e+03 pdb=" H8 G C 8 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 9 " 0.019 2.00e-02 2.50e+03 1.08e-02 3.23e+00 pdb=" N1 U G 9 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U G 9 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U G 9 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U G 9 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U G 9 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U G 9 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U G 9 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U G 9 " 0.000 2.00e-02 2.50e+03 pdb=" H5 U G 9 " 0.002 2.00e-02 2.50e+03 pdb=" H6 U G 9 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 464 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO E 465 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 465 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 465 " 0.025 5.00e-02 4.00e+02 ... (remaining 4513 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 318 2.05 - 2.69: 52360 2.69 - 3.33: 101765 3.33 - 3.96: 136430 3.96 - 4.60: 210385 Nonbonded interactions: 501258 Sorted by model distance: nonbonded pdb=" O ASN I 160 " pdb="HD21 ASN I 160 " model vdw 1.417 2.450 nonbonded pdb=" H8 A G 16 " pdb=" H5 U G 17 " model vdw 1.788 2.100 nonbonded pdb=" H8 A C 16 " pdb=" H5 U C 17 " model vdw 1.789 2.100 nonbonded pdb=" OE1 GLU E 395 " pdb=" H GLU E 395 " model vdw 1.795 2.450 nonbonded pdb=" HD1 HIS E 110 " pdb=" HG SER E 206 " model vdw 1.807 2.100 ... (remaining 501253 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' and (resid 1 through 535 or resid 542 through 586)) selection = chain 'E' selection = (chain 'I' and (resid 1 through 535 or resid 542 through 586)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.180 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 38.000 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.004 0.045 19666 Z= 0.187 Angle : 0.562 7.474 27531 Z= 0.304 Chirality : 0.040 0.194 3226 Planarity : 0.004 0.044 2668 Dihedral : 21.787 175.657 8714 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.34 % Allowed : 16.91 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.17 (0.21), residues: 1734 helix: 0.72 (0.18), residues: 845 sheet: -0.11 (0.38), residues: 188 loop : -1.08 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 132 TYR 0.020 0.002 TYR I 273 PHE 0.013 0.001 PHE I 357 HIS 0.004 0.001 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00400 (19666) covalent geometry : angle 0.56157 (27531) hydrogen bonds : bond 0.11510 ( 857) hydrogen bonds : angle 5.90490 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8091 (m-30) cc_final: 0.7794 (m-30) REVERT: A 256 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: E 116 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8678 (mm) REVERT: E 486 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.3762 (pmm) REVERT: E 579 HIS cc_start: 0.6622 (t-170) cc_final: 0.6342 (t-170) REVERT: I 24 ASP cc_start: 0.7919 (t0) cc_final: 0.7565 (t0) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 1.0910 time to fit residues: 206.9989 Evaluate side-chains 162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 463 THR Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 366 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 179 ASN I 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141948 restraints weight = 49175.280| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.33 r_work: 0.3161 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19666 Z= 0.207 Angle : 0.564 7.525 27531 Z= 0.307 Chirality : 0.041 0.199 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.767 175.714 5167 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.04 % Allowed : 17.04 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.04 (0.21), residues: 1734 helix: 0.91 (0.18), residues: 854 sheet: -0.20 (0.38), residues: 192 loop : -1.12 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 254 TYR 0.016 0.002 TYR E 446 PHE 0.013 0.001 PHE E 95 HIS 0.003 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00444 (19666) covalent geometry : angle 0.56421 (27531) hydrogen bonds : bond 0.05127 ( 857) hydrogen bonds : angle 4.85667 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7590 (mm110) REVERT: A 78 ASP cc_start: 0.8077 (m-30) cc_final: 0.7799 (m-30) REVERT: A 407 GLU cc_start: 0.6660 (pm20) cc_final: 0.6346 (pm20) REVERT: A 581 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7426 (ttpp) REVERT: E 486 MET cc_start: 0.5037 (mtt) cc_final: 0.3776 (pmm) REVERT: E 491 TYR cc_start: 0.6590 (p90) cc_final: 0.6374 (p90) REVERT: I 24 ASP cc_start: 0.7916 (t0) cc_final: 0.7564 (t0) outliers start: 32 outliers final: 17 residues processed: 177 average time/residue: 1.0762 time to fit residues: 220.8245 Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN E 179 ASN I 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141852 restraints weight = 48859.395| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.49 r_work: 0.3154 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19666 Z= 0.184 Angle : 0.547 7.517 27531 Z= 0.298 Chirality : 0.040 0.197 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.695 176.073 5143 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.23 % Allowed : 16.53 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.05 (0.21), residues: 1734 helix: 1.03 (0.18), residues: 852 sheet: -0.20 (0.38), residues: 192 loop : -1.13 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.016 0.002 TYR I 273 PHE 0.012 0.001 PHE A 46 HIS 0.003 0.001 HIS I 110 Details of bonding type rmsd covalent geometry : bond 0.00393 (19666) covalent geometry : angle 0.54747 (27531) hydrogen bonds : bond 0.04793 ( 857) hydrogen bonds : angle 4.62158 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7586 (mm110) REVERT: A 78 ASP cc_start: 0.8055 (m-30) cc_final: 0.7773 (m-30) REVERT: A 398 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7553 (mtt90) REVERT: A 407 GLU cc_start: 0.6745 (pm20) cc_final: 0.6337 (pm20) REVERT: A 581 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7698 (ttmm) REVERT: E 187 LYS cc_start: 0.8576 (mttm) cc_final: 0.7963 (mtmt) REVERT: E 486 MET cc_start: 0.4936 (mtt) cc_final: 0.3664 (pmm) REVERT: E 491 TYR cc_start: 0.6603 (p90) cc_final: 0.6360 (p90) REVERT: I 24 ASP cc_start: 0.7880 (t0) cc_final: 0.7518 (t0) REVERT: I 570 PHE cc_start: 0.7862 (m-10) cc_final: 0.7652 (m-10) outliers start: 35 outliers final: 21 residues processed: 189 average time/residue: 1.0552 time to fit residues: 230.8885 Evaluate side-chains 174 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN I 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142489 restraints weight = 48969.339| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.29 r_work: 0.3166 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19666 Z= 0.199 Angle : 0.557 7.502 27531 Z= 0.303 Chirality : 0.041 0.198 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.690 175.957 5142 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.55 % Allowed : 16.15 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.14 (0.21), residues: 1734 helix: 1.09 (0.18), residues: 840 sheet: -0.22 (0.38), residues: 192 loop : -1.00 (0.26), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 254 TYR 0.017 0.002 TYR I 273 PHE 0.014 0.001 PHE A 29 HIS 0.003 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00426 (19666) covalent geometry : angle 0.55700 (27531) hydrogen bonds : bond 0.04824 ( 857) hydrogen bonds : angle 4.59312 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7576 (mm110) REVERT: A 78 ASP cc_start: 0.8070 (m-30) cc_final: 0.7795 (m-30) REVERT: A 398 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7450 (mtt90) REVERT: A 407 GLU cc_start: 0.6854 (pm20) cc_final: 0.6416 (pm20) REVERT: E 32 ASN cc_start: 0.5839 (OUTLIER) cc_final: 0.5533 (t0) REVERT: E 116 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8714 (mm) REVERT: E 187 LYS cc_start: 0.8535 (mttm) cc_final: 0.7981 (mtmt) REVERT: E 216 MET cc_start: 0.9066 (mmp) cc_final: 0.8617 (mmt) REVERT: E 486 MET cc_start: 0.5013 (mtt) cc_final: 0.3660 (pmm) REVERT: I 24 ASP cc_start: 0.7853 (t0) cc_final: 0.7488 (t0) outliers start: 40 outliers final: 25 residues processed: 189 average time/residue: 0.9832 time to fit residues: 215.1960 Evaluate side-chains 179 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 411 ASN I 92 ASN I 160 ASN I 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.186262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137851 restraints weight = 48962.763| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.45 r_work: 0.3127 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19666 Z= 0.291 Angle : 0.620 7.424 27531 Z= 0.335 Chirality : 0.044 0.217 3226 Planarity : 0.005 0.046 2668 Dihedral : 23.792 177.667 5142 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.32 % Allowed : 15.57 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.20 (0.21), residues: 1734 helix: 0.84 (0.18), residues: 852 sheet: -0.33 (0.38), residues: 192 loop : -1.25 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.027 0.002 TYR I 273 PHE 0.018 0.002 PHE E 95 HIS 0.005 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00634 (19666) covalent geometry : angle 0.62035 (27531) hydrogen bonds : bond 0.05465 ( 857) hydrogen bonds : angle 4.72783 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7826 (mm110) REVERT: A 78 ASP cc_start: 0.8128 (m-30) cc_final: 0.7842 (m-30) REVERT: A 398 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7576 (mtt90) REVERT: A 407 GLU cc_start: 0.6883 (pm20) cc_final: 0.6415 (pm20) REVERT: E 1 MET cc_start: 0.4160 (OUTLIER) cc_final: 0.3801 (mpp) REVERT: E 32 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.5563 (t0) REVERT: E 116 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8688 (mm) REVERT: E 187 LYS cc_start: 0.8546 (mttm) cc_final: 0.7986 (mtmt) REVERT: E 216 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8712 (mmt) REVERT: E 486 MET cc_start: 0.5002 (mtt) cc_final: 0.3607 (pmm) REVERT: E 491 TYR cc_start: 0.6607 (p90) cc_final: 0.6378 (p90) REVERT: I 24 ASP cc_start: 0.7887 (t0) cc_final: 0.7528 (t0) outliers start: 52 outliers final: 28 residues processed: 199 average time/residue: 1.0200 time to fit residues: 234.7011 Evaluate side-chains 187 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 140 ASN A 179 ASN A 327 ASN I 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.189431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155029 restraints weight = 49394.528| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 0.92 r_work: 0.3221 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19666 Z= 0.140 Angle : 0.531 7.382 27531 Z= 0.288 Chirality : 0.039 0.187 3226 Planarity : 0.004 0.046 2668 Dihedral : 23.680 176.754 5142 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.91 % Allowed : 17.42 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.21), residues: 1734 helix: 1.17 (0.19), residues: 842 sheet: -0.22 (0.38), residues: 192 loop : -0.98 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.016 0.001 TYR I 273 PHE 0.017 0.001 PHE A 29 HIS 0.004 0.001 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00290 (19666) covalent geometry : angle 0.53102 (27531) hydrogen bonds : bond 0.04336 ( 857) hydrogen bonds : angle 4.46465 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8064 (m-30) cc_final: 0.7774 (m-30) REVERT: A 398 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7599 (mtt90) REVERT: A 407 GLU cc_start: 0.7036 (pm20) cc_final: 0.6573 (pm20) REVERT: A 581 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7548 (ttpp) REVERT: E 32 ASN cc_start: 0.5887 (OUTLIER) cc_final: 0.5597 (t0) REVERT: E 116 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8700 (mm) REVERT: E 187 LYS cc_start: 0.8476 (mttm) cc_final: 0.7943 (mtmt) REVERT: E 216 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8533 (mmt) REVERT: E 486 MET cc_start: 0.5111 (mtt) cc_final: 0.3677 (pmm) REVERT: I 24 ASP cc_start: 0.7807 (t0) cc_final: 0.7465 (t0) REVERT: I 383 LYS cc_start: 0.7164 (mtpt) cc_final: 0.6950 (mmtp) outliers start: 30 outliers final: 16 residues processed: 186 average time/residue: 1.0109 time to fit residues: 216.7269 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 187 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.193990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144693 restraints weight = 50621.395| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.61 r_work: 0.3364 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19666 Z= 0.239 Angle : 0.583 7.634 27531 Z= 0.315 Chirality : 0.042 0.205 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.707 176.188 5141 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.17 % Allowed : 17.74 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.07 (0.21), residues: 1734 helix: 1.05 (0.18), residues: 840 sheet: -0.27 (0.38), residues: 192 loop : -1.05 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.025 0.002 TYR I 273 PHE 0.017 0.002 PHE E 549 HIS 0.004 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00519 (19666) covalent geometry : angle 0.58290 (27531) hydrogen bonds : bond 0.05036 ( 857) hydrogen bonds : angle 4.57950 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7563 (mm110) REVERT: A 78 ASP cc_start: 0.8067 (m-30) cc_final: 0.7818 (m-30) REVERT: A 398 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7600 (mtt90) REVERT: A 407 GLU cc_start: 0.6898 (pm20) cc_final: 0.6451 (pm20) REVERT: A 581 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7372 (tttm) REVERT: E 32 ASN cc_start: 0.5916 (OUTLIER) cc_final: 0.5609 (t0) REVERT: E 116 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8724 (mm) REVERT: E 187 LYS cc_start: 0.8423 (mttm) cc_final: 0.7840 (mtmt) REVERT: E 216 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8739 (mmt) REVERT: E 486 MET cc_start: 0.5059 (mtt) cc_final: 0.3645 (pmm) REVERT: I 24 ASP cc_start: 0.7776 (t0) cc_final: 0.7434 (t0) outliers start: 34 outliers final: 22 residues processed: 185 average time/residue: 1.0085 time to fit residues: 215.4096 Evaluate side-chains 181 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 160 ASN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 411 ASN I 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.193329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145159 restraints weight = 50568.032| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.54 r_work: 0.3359 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19666 Z= 0.279 Angle : 0.613 7.506 27531 Z= 0.330 Chirality : 0.044 0.211 3226 Planarity : 0.005 0.044 2668 Dihedral : 23.747 176.528 5138 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.30 % Allowed : 17.49 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.15 (0.21), residues: 1734 helix: 0.88 (0.18), residues: 852 sheet: -0.30 (0.38), residues: 192 loop : -1.24 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.029 0.002 TYR I 273 PHE 0.016 0.002 PHE E 95 HIS 0.004 0.001 HIS I 110 Details of bonding type rmsd covalent geometry : bond 0.00607 (19666) covalent geometry : angle 0.61321 (27531) hydrogen bonds : bond 0.05245 ( 857) hydrogen bonds : angle 4.65162 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8070 (m-30) cc_final: 0.7800 (m-30) REVERT: A 398 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7656 (mtt90) REVERT: A 407 GLU cc_start: 0.6939 (pm20) cc_final: 0.6467 (pm20) REVERT: E 32 ASN cc_start: 0.5953 (OUTLIER) cc_final: 0.5633 (t0) REVERT: E 116 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8691 (mm) REVERT: E 187 LYS cc_start: 0.8443 (mttm) cc_final: 0.7884 (mtmt) REVERT: E 216 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8800 (mmt) REVERT: E 486 MET cc_start: 0.5155 (mtt) cc_final: 0.3738 (pmm) REVERT: I 1 MET cc_start: 0.4099 (tpt) cc_final: 0.3806 (tpt) REVERT: I 24 ASP cc_start: 0.7743 (t0) cc_final: 0.7410 (t0) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 1.0488 time to fit residues: 224.3161 Evaluate side-chains 179 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.195752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147496 restraints weight = 51099.486| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.51 r_work: 0.3409 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19666 Z= 0.135 Angle : 0.533 7.399 27531 Z= 0.289 Chirality : 0.039 0.187 3226 Planarity : 0.004 0.046 2668 Dihedral : 23.659 176.629 5138 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.40 % Allowed : 18.83 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.21), residues: 1734 helix: 1.20 (0.19), residues: 842 sheet: -0.23 (0.38), residues: 192 loop : -0.97 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.017 0.001 TYR I 273 PHE 0.023 0.001 PHE E 549 HIS 0.003 0.001 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00279 (19666) covalent geometry : angle 0.53299 (27531) hydrogen bonds : bond 0.04308 ( 857) hydrogen bonds : angle 4.43798 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8039 (m-30) cc_final: 0.7784 (m-30) REVERT: A 398 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7615 (mtt90) REVERT: A 407 GLU cc_start: 0.6956 (pm20) cc_final: 0.6496 (pm20) REVERT: A 581 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7593 (ttpp) REVERT: E 32 ASN cc_start: 0.5874 (OUTLIER) cc_final: 0.5567 (t0) REVERT: E 187 LYS cc_start: 0.8427 (mttm) cc_final: 0.7858 (mtmt) REVERT: E 216 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8600 (mmt) REVERT: E 486 MET cc_start: 0.5114 (mtt) cc_final: 0.3728 (pmm) REVERT: I 24 ASP cc_start: 0.7758 (t0) cc_final: 0.7420 (t0) outliers start: 22 outliers final: 14 residues processed: 170 average time/residue: 1.0384 time to fit residues: 202.3442 Evaluate side-chains 165 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.194878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147342 restraints weight = 51046.098| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.48 r_work: 0.3393 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19666 Z= 0.166 Angle : 0.543 7.600 27531 Z= 0.294 Chirality : 0.039 0.192 3226 Planarity : 0.004 0.046 2668 Dihedral : 23.622 176.862 5138 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.34 % Allowed : 18.89 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.21), residues: 1734 helix: 1.19 (0.18), residues: 842 sheet: -0.23 (0.38), residues: 192 loop : -0.97 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.019 0.002 TYR I 273 PHE 0.017 0.001 PHE A 29 HIS 0.003 0.001 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00353 (19666) covalent geometry : angle 0.54253 (27531) hydrogen bonds : bond 0.04516 ( 857) hydrogen bonds : angle 4.43853 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8071 (m-30) cc_final: 0.7803 (m-30) REVERT: A 398 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7616 (mtt90) REVERT: A 407 GLU cc_start: 0.6955 (pm20) cc_final: 0.6506 (pm20) REVERT: A 581 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7229 (tttm) REVERT: E 32 ASN cc_start: 0.5900 (OUTLIER) cc_final: 0.5595 (t0) REVERT: E 116 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8721 (mm) REVERT: E 187 LYS cc_start: 0.8431 (mttm) cc_final: 0.7867 (mtmt) REVERT: E 216 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8592 (mmt) REVERT: E 486 MET cc_start: 0.5057 (mtt) cc_final: 0.3729 (pmm) REVERT: I 24 ASP cc_start: 0.7797 (t0) cc_final: 0.7456 (t0) outliers start: 21 outliers final: 17 residues processed: 166 average time/residue: 1.0392 time to fit residues: 198.6264 Evaluate side-chains 167 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 160 ASN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.194812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146865 restraints weight = 50877.640| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.62 r_work: 0.3390 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 19666 Z= 0.209 Angle : 0.706 59.194 27531 Z= 0.409 Chirality : 0.042 0.822 3226 Planarity : 0.004 0.053 2668 Dihedral : 23.623 176.853 5138 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 1.34 % Allowed : 18.70 % Favored : 79.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.21), residues: 1734 helix: 1.19 (0.18), residues: 842 sheet: -0.22 (0.38), residues: 192 loop : -0.97 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.017 0.002 TYR I 273 PHE 0.016 0.001 PHE A 29 HIS 0.003 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00431 (19666) covalent geometry : angle 0.70625 (27531) hydrogen bonds : bond 0.04539 ( 857) hydrogen bonds : angle 4.43953 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12143.83 seconds wall clock time: 206 minutes 2.16 seconds (12362.16 seconds total)