Starting phenix.real_space_refine on Thu Mar 5 16:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pby_20295/03_2026/6pby_20295.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pby_20295/03_2026/6pby_20295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pby_20295/03_2026/6pby_20295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pby_20295/03_2026/6pby_20295.map" model { file = "/net/cci-nas-00/data/ceres_data/6pby_20295/03_2026/6pby_20295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pby_20295/03_2026/6pby_20295.cif" } resolution = 3.67 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15412 2.51 5 N 3964 2.21 5 O 4328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23832 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5088 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 22, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 14, 'ASN:plan1': 5, 'ASP:plan': 9, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 870 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 149 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 5.01, per 1000 atoms: 0.21 Number of scatterers: 23832 At special positions: 0 Unit cell: (155, 155, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4328 8.00 N 3964 7.00 C 15412 6.00 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: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 62.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.884A pdb=" N GLN A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.950A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.809A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.930A pdb=" N CYS A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP B 20 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY B 113 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.734A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.689A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.734A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP F 20 " --> pdb=" O PHE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU F 83 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.566A pdb=" N GLY F 113 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.735A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP H 20 " --> pdb=" O PHE H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU H 83 " --> pdb=" O THR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY H 113 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.735A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 138 removed outlier: 3.885A pdb=" N GLN C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL C 328 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 379 removed outlier: 3.949A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.808A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 133 through 138 removed outlier: 3.885A pdb=" N GLN E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 242 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL E 328 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 379 removed outlier: 3.950A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 418 through 435 Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.810A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 521 Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS E 532 " --> pdb=" O VAL E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 620 through 625 Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 696 Processing helix chain 'E' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 133 through 138 removed outlier: 3.884A pdb=" N GLN G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 242 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS G 293 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE G 298 " --> pdb=" O THR G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 379 removed outlier: 3.951A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 418 through 435 Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.809A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN G 481 " --> pdb=" O GLN G 477 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 521 Processing helix chain 'G' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS G 532 " --> pdb=" O VAL G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 620 through 625 Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 696 Processing helix chain 'G' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A 45 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE A 30 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS A 643 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 594 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A 645 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS A 592 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 611 removed outlier: 6.573A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER C 45 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE C 30 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS C 643 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL C 594 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 645 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS C 592 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 606 through 611 removed outlier: 6.573A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER E 45 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE E 30 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 571 through 575 removed outlier: 6.830A pdb=" N HIS E 643 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL E 594 " --> pdb=" O HIS E 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 645 " --> pdb=" O CYS E 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS E 592 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 672 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 606 through 611 removed outlier: 6.572A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU G 32 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER G 45 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE G 30 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS G 643 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL G 594 " --> pdb=" O HIS G 643 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE G 645 " --> pdb=" O CYS G 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS G 592 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR G 672 " --> pdb=" O VAL G 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 606 through 611 removed outlier: 6.572A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1512 hydrogen bonds defined for protein. 4332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7427 1.34 - 1.46: 5499 1.46 - 1.58: 11250 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 24372 Sorted by residual: bond pdb=" CB ASN G 441 " pdb=" CG ASN G 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ASN E 441 " pdb=" CG ASN E 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN A 441 " pdb=" CG ASN A 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN C 441 " pdb=" CG ASN C 441 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.75e+00 bond pdb=" CG1 ILE E 456 " pdb=" CD1 ILE E 456 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 ... (remaining 24367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 32520 2.57 - 5.15: 671 5.15 - 7.72: 93 7.72 - 10.30: 12 10.30 - 12.87: 12 Bond angle restraints: 33308 Sorted by residual: angle pdb=" CA ARG G 387 " pdb=" CB ARG G 387 " pdb=" CG ARG G 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG C 387 " pdb=" CB ARG C 387 " pdb=" CG ARG C 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG E 387 " pdb=" CB ARG E 387 " pdb=" CG ARG E 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG A 387 " pdb=" CB ARG A 387 " pdb=" CG ARG A 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB MET A 366 " pdb=" CG MET A 366 " pdb=" SD MET A 366 " ideal model delta sigma weight residual 112.70 125.57 -12.87 3.00e+00 1.11e-01 1.84e+01 ... (remaining 33303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 12666 17.14 - 34.29: 1162 34.29 - 51.43: 236 51.43 - 68.57: 44 68.57 - 85.72: 12 Dihedral angle restraints: 14120 sinusoidal: 4560 harmonic: 9560 Sorted by residual: dihedral pdb=" CA ILE A 194 " pdb=" C ILE A 194 " pdb=" N LEU A 195 " pdb=" CA LEU A 195 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE C 194 " pdb=" C ILE C 194 " pdb=" N LEU C 195 " pdb=" CA LEU C 195 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE E 194 " pdb=" C ILE E 194 " pdb=" N LEU E 195 " pdb=" CA LEU E 195 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2750 0.052 - 0.103: 886 0.103 - 0.155: 240 0.155 - 0.206: 32 0.206 - 0.258: 20 Chirality restraints: 3928 Sorted by residual: chirality pdb=" CB ILE G 140 " pdb=" CA ILE G 140 " pdb=" CG1 ILE G 140 " pdb=" CG2 ILE G 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 140 " pdb=" CA ILE C 140 " pdb=" CG1 ILE C 140 " pdb=" CG2 ILE C 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE A 140 " pdb=" CA ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CG2 ILE A 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3925 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 366 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C MET E 366 " -0.052 2.00e-02 2.50e+03 pdb=" O MET E 366 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA E 367 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 366 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C MET G 366 " 0.051 2.00e-02 2.50e+03 pdb=" O MET G 366 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA G 367 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 366 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C MET A 366 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A 366 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 367 " -0.018 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5864 2.78 - 3.31: 22799 3.31 - 3.84: 40975 3.84 - 4.37: 44736 4.37 - 4.90: 77811 Nonbonded interactions: 192185 Sorted by model distance: nonbonded pdb=" OH TYR A 198 " pdb=" OE1 GLU C 600 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR C 198 " pdb=" OE1 GLU E 600 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR E 198 " pdb=" OE1 GLU G 600 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR G 446 " pdb=" OE1 GLU G 449 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" OE1 GLU A 449 " model vdw 2.298 3.040 ... (remaining 192180 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 24372 Z= 0.351 Angle : 0.927 12.870 33308 Z= 0.499 Chirality : 0.056 0.258 3928 Planarity : 0.007 0.055 4248 Dihedral : 14.382 85.718 7920 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -3.45 (0.12), residues: 3220 helix: -2.06 (0.09), residues: 1788 sheet: -2.42 (0.28), residues: 228 loop : -2.36 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 24 TYR 0.039 0.003 TYR C 464 PHE 0.032 0.003 PHE E 475 TRP 0.012 0.003 TRP E 222 HIS 0.010 0.002 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00793 (24372) covalent geometry : angle 0.92692 (33308) hydrogen bonds : bond 0.11124 ( 1512) hydrogen bonds : angle 5.60102 ( 4332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8145 (t80) cc_final: 0.7903 (t80) REVERT: A 90 TYR cc_start: 0.7922 (m-80) cc_final: 0.7720 (m-10) REVERT: A 109 PHE cc_start: 0.7947 (m-80) cc_final: 0.7590 (m-10) REVERT: A 344 TYR cc_start: 0.4842 (m-80) cc_final: 0.4347 (m-80) REVERT: A 347 TYR cc_start: 0.4691 (m-80) cc_final: 0.4295 (t80) REVERT: A 376 TYR cc_start: 0.7854 (t80) cc_final: 0.7586 (t80) REVERT: A 519 MET cc_start: 0.7172 (ttm) cc_final: 0.6798 (tmm) REVERT: A 575 CYS cc_start: 0.6318 (m) cc_final: 0.5751 (p) REVERT: B 107 HIS cc_start: 0.6943 (t-90) cc_final: 0.6574 (t-170) REVERT: B 123 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 107 HIS cc_start: 0.6469 (t-90) cc_final: 0.6266 (t70) REVERT: D 123 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 127 GLU cc_start: 0.4810 (tt0) cc_final: 0.4575 (pt0) REVERT: H 123 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 17 PHE cc_start: 0.8112 (t80) cc_final: 0.7869 (t80) REVERT: C 90 TYR cc_start: 0.7921 (m-80) cc_final: 0.7719 (m-10) REVERT: C 109 PHE cc_start: 0.7940 (m-80) cc_final: 0.7557 (m-10) REVERT: C 344 TYR cc_start: 0.4849 (m-80) cc_final: 0.4361 (m-80) REVERT: C 347 TYR cc_start: 0.4735 (m-80) cc_final: 0.4304 (t80) REVERT: C 398 ASP cc_start: 0.7699 (t70) cc_final: 0.7498 (t0) REVERT: C 519 MET cc_start: 0.7129 (ttm) cc_final: 0.6752 (tmm) REVERT: C 575 CYS cc_start: 0.6231 (m) cc_final: 0.5657 (p) REVERT: C 615 ASP cc_start: 0.7418 (m-30) cc_final: 0.7105 (m-30) REVERT: E 17 PHE cc_start: 0.8110 (t80) cc_final: 0.7868 (t80) REVERT: E 109 PHE cc_start: 0.7907 (m-80) cc_final: 0.7550 (m-10) REVERT: E 344 TYR cc_start: 0.4860 (m-80) cc_final: 0.4372 (m-80) REVERT: E 347 TYR cc_start: 0.4745 (m-80) cc_final: 0.4325 (t80) REVERT: E 519 MET cc_start: 0.7114 (ttm) cc_final: 0.6722 (tmm) REVERT: E 575 CYS cc_start: 0.6151 (m) cc_final: 0.5575 (p) REVERT: E 615 ASP cc_start: 0.7511 (m-30) cc_final: 0.7216 (m-30) REVERT: E 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7713 (mm-40) REVERT: G 17 PHE cc_start: 0.8119 (t80) cc_final: 0.7877 (t80) REVERT: G 109 PHE cc_start: 0.7905 (m-80) cc_final: 0.7544 (m-10) REVERT: G 344 TYR cc_start: 0.4850 (m-80) cc_final: 0.4361 (m-80) REVERT: G 347 TYR cc_start: 0.4740 (m-80) cc_final: 0.4326 (t80) REVERT: G 519 MET cc_start: 0.7102 (ttm) cc_final: 0.6709 (tmm) REVERT: G 575 CYS cc_start: 0.6162 (m) cc_final: 0.5579 (p) REVERT: G 615 ASP cc_start: 0.7461 (m-30) cc_final: 0.7150 (m-30) REVERT: G 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7715 (mm-40) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.1574 time to fit residues: 122.9487 Evaluate side-chains 328 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN A 343 HIS A 667 ASN B 107 HIS D 107 HIS F 107 HIS C 93 ASN C 343 HIS C 667 ASN E 93 ASN E 343 HIS E 667 ASN G 20 ASN G 93 ASN G 343 HIS G 667 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.141853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113584 restraints weight = 51835.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112443 restraints weight = 38533.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113215 restraints weight = 38662.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114178 restraints weight = 25602.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114308 restraints weight = 22867.209| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24372 Z= 0.140 Angle : 0.611 12.659 33308 Z= 0.319 Chirality : 0.042 0.217 3928 Planarity : 0.004 0.042 4248 Dihedral : 5.053 15.841 3456 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.72 % Allowed : 15.13 % Favored : 83.15 % 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: -1.69 (0.13), residues: 3220 helix: -0.42 (0.11), residues: 1824 sheet: -2.05 (0.30), residues: 204 loop : -1.91 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.017 0.002 TYR C 464 PHE 0.015 0.002 PHE C 475 TRP 0.010 0.001 TRP C 222 HIS 0.017 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00300 (24372) covalent geometry : angle 0.61089 (33308) hydrogen bonds : bond 0.03902 ( 1512) hydrogen bonds : angle 4.74765 ( 4332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 391 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8167 (m-80) cc_final: 0.7933 (m-10) REVERT: A 344 TYR cc_start: 0.7237 (m-80) cc_final: 0.6914 (m-80) REVERT: A 347 TYR cc_start: 0.6394 (m-80) cc_final: 0.6145 (t80) REVERT: A 487 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 510 MET cc_start: 0.8718 (mmm) cc_final: 0.8444 (mmm) REVERT: B 123 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 131 ASP cc_start: 0.7913 (p0) cc_final: 0.7668 (p0) REVERT: D 123 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8038 (tm-30) REVERT: F 138 TYR cc_start: 0.7825 (t80) cc_final: 0.7545 (t80) REVERT: H 123 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 109 PHE cc_start: 0.8169 (m-80) cc_final: 0.7928 (m-10) REVERT: C 344 TYR cc_start: 0.7225 (m-80) cc_final: 0.6912 (m-80) REVERT: C 347 TYR cc_start: 0.6524 (m-80) cc_final: 0.6204 (t80) REVERT: C 487 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7942 (tm-30) REVERT: C 510 MET cc_start: 0.8749 (mmm) cc_final: 0.8458 (mmm) REVERT: E 109 PHE cc_start: 0.8168 (m-80) cc_final: 0.7924 (m-10) REVERT: E 261 PHE cc_start: 0.8082 (m-10) cc_final: 0.7844 (m-10) REVERT: E 344 TYR cc_start: 0.7236 (m-80) cc_final: 0.6917 (m-80) REVERT: E 347 TYR cc_start: 0.6600 (m-80) cc_final: 0.6197 (t80) REVERT: E 487 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7858 (tp30) REVERT: E 510 MET cc_start: 0.8726 (mmm) cc_final: 0.8485 (mmm) REVERT: G 109 PHE cc_start: 0.8127 (m-80) cc_final: 0.7918 (m-10) REVERT: G 261 PHE cc_start: 0.8057 (m-10) cc_final: 0.7824 (m-10) REVERT: G 344 TYR cc_start: 0.7183 (m-80) cc_final: 0.6868 (m-80) REVERT: G 347 TYR cc_start: 0.6485 (m-80) cc_final: 0.6217 (t80) REVERT: G 487 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7935 (tm-30) REVERT: G 510 MET cc_start: 0.8739 (mmm) cc_final: 0.8465 (mmm) outliers start: 38 outliers final: 14 residues processed: 411 average time/residue: 0.1278 time to fit residues: 88.0483 Evaluate side-chains 349 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 335 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 645 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 233 optimal weight: 0.5980 chunk 167 optimal weight: 7.9990 chunk 294 optimal weight: 0.0770 chunk 232 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 chunk 270 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 overall best weight: 3.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.138485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111358 restraints weight = 52298.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109889 restraints weight = 46128.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110928 restraints weight = 50321.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111189 restraints weight = 31086.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112983 restraints weight = 27054.693| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24372 Z= 0.266 Angle : 0.689 14.410 33308 Z= 0.353 Chirality : 0.044 0.199 3928 Planarity : 0.004 0.046 4248 Dihedral : 4.894 15.881 3456 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.36 % Allowed : 16.71 % Favored : 80.93 % 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: -0.96 (0.14), residues: 3220 helix: 0.19 (0.12), residues: 1832 sheet: -2.18 (0.33), residues: 160 loop : -1.62 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 675 TYR 0.020 0.002 TYR E 230 PHE 0.028 0.002 PHE H 68 TRP 0.012 0.002 TRP E 517 HIS 0.009 0.002 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00601 (24372) covalent geometry : angle 0.68916 (33308) hydrogen bonds : bond 0.03841 ( 1512) hydrogen bonds : angle 4.70846 ( 4332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8034 (m-80) cc_final: 0.7773 (m-10) REVERT: A 347 TYR cc_start: 0.6547 (m-80) cc_final: 0.6330 (t80) REVERT: A 487 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8036 (tm-30) REVERT: D 123 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8052 (tm-30) REVERT: H 123 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8185 (tm-30) REVERT: C 109 PHE cc_start: 0.8035 (m-80) cc_final: 0.7761 (m-10) REVERT: C 344 TYR cc_start: 0.7393 (m-80) cc_final: 0.7156 (m-80) REVERT: C 487 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7990 (tm-30) REVERT: E 109 PHE cc_start: 0.8031 (m-80) cc_final: 0.7774 (m-10) REVERT: E 227 LEU cc_start: 0.9163 (mm) cc_final: 0.8948 (mt) REVERT: E 264 ASP cc_start: 0.7183 (t0) cc_final: 0.6716 (t0) REVERT: E 487 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7976 (tm-30) REVERT: G 109 PHE cc_start: 0.8033 (m-80) cc_final: 0.7787 (m-10) REVERT: G 227 LEU cc_start: 0.9163 (mm) cc_final: 0.8936 (mt) REVERT: G 264 ASP cc_start: 0.7174 (t0) cc_final: 0.6754 (t0) REVERT: G 347 TYR cc_start: 0.6482 (m-80) cc_final: 0.6254 (t80) REVERT: G 487 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8010 (tm-30) outliers start: 52 outliers final: 31 residues processed: 367 average time/residue: 0.1249 time to fit residues: 77.4748 Evaluate side-chains 327 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 645 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 196 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 HIS ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 483 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.141091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113830 restraints weight = 51759.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112239 restraints weight = 43917.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113210 restraints weight = 48469.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113734 restraints weight = 29647.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115287 restraints weight = 25536.875| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24372 Z= 0.137 Angle : 0.599 12.278 33308 Z= 0.309 Chirality : 0.041 0.158 3928 Planarity : 0.004 0.062 4248 Dihedral : 4.600 15.565 3456 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.13 % Allowed : 18.70 % Favored : 79.17 % 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: -0.43 (0.15), residues: 3220 helix: 0.68 (0.12), residues: 1836 sheet: -1.76 (0.34), residues: 180 loop : -1.50 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 336 TYR 0.016 0.001 TYR G 230 PHE 0.016 0.001 PHE G 452 TRP 0.013 0.001 TRP G 222 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00309 (24372) covalent geometry : angle 0.59868 (33308) hydrogen bonds : bond 0.03498 ( 1512) hydrogen bonds : angle 4.49647 ( 4332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 344 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7985 (m-80) cc_final: 0.7725 (m-10) REVERT: A 347 TYR cc_start: 0.6523 (m-80) cc_final: 0.6315 (t80) REVERT: A 487 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 123 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8060 (tm-30) REVERT: H 123 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 109 PHE cc_start: 0.7991 (m-80) cc_final: 0.7740 (m-10) REVERT: C 344 TYR cc_start: 0.7234 (m-80) cc_final: 0.7021 (m-80) REVERT: C 487 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7974 (tm-30) REVERT: E 109 PHE cc_start: 0.7997 (m-80) cc_final: 0.7776 (m-10) REVERT: E 487 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7942 (tm-30) REVERT: G 109 PHE cc_start: 0.7964 (m-80) cc_final: 0.7743 (m-10) REVERT: G 487 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7958 (tm-30) outliers start: 47 outliers final: 22 residues processed: 379 average time/residue: 0.1251 time to fit residues: 81.3204 Evaluate side-chains 323 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 301 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain G residue 483 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 99 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 HIS ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.136235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109216 restraints weight = 52015.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107957 restraints weight = 47169.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108791 restraints weight = 51604.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109351 restraints weight = 30833.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.110623 restraints weight = 26397.325| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 24372 Z= 0.334 Angle : 0.735 13.967 33308 Z= 0.377 Chirality : 0.046 0.236 3928 Planarity : 0.004 0.053 4248 Dihedral : 4.775 16.998 3456 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.62 % Allowed : 19.38 % Favored : 76.99 % 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: -0.41 (0.15), residues: 3220 helix: 0.63 (0.12), residues: 1836 sheet: -1.91 (0.34), residues: 180 loop : -1.36 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 336 TYR 0.025 0.002 TYR G 230 PHE 0.022 0.002 PHE C 17 TRP 0.012 0.002 TRP E 391 HIS 0.011 0.001 HIS C 552 Details of bonding type rmsd covalent geometry : bond 0.00752 (24372) covalent geometry : angle 0.73489 (33308) hydrogen bonds : bond 0.03850 ( 1512) hydrogen bonds : angle 4.72083 ( 4332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 303 time to evaluate : 0.950 Fit side-chains REVERT: A 109 PHE cc_start: 0.8063 (m-80) cc_final: 0.7787 (m-10) REVERT: A 347 TYR cc_start: 0.6589 (m-80) cc_final: 0.6317 (t80) REVERT: A 458 MET cc_start: 0.8627 (tpt) cc_final: 0.8397 (tpp) REVERT: A 487 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8052 (tm-30) REVERT: D 123 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7906 (tm-30) REVERT: H 123 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 109 PHE cc_start: 0.8002 (m-80) cc_final: 0.7760 (m-10) REVERT: C 264 ASP cc_start: 0.7791 (t0) cc_final: 0.7530 (m-30) REVERT: E 109 PHE cc_start: 0.8105 (m-80) cc_final: 0.7836 (m-10) REVERT: G 109 PHE cc_start: 0.8075 (m-80) cc_final: 0.7832 (m-10) REVERT: G 458 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8160 (tpp) outliers start: 80 outliers final: 56 residues processed: 360 average time/residue: 0.1215 time to fit residues: 76.1664 Evaluate side-chains 334 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 441 ASN Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 441 ASN Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 645 ILE Chi-restraints excluded: chain G residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 24 optimal weight: 3.9990 chunk 276 optimal weight: 0.4980 chunk 135 optimal weight: 0.0770 chunk 211 optimal weight: 0.5980 chunk 288 optimal weight: 0.9980 chunk 263 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 483 ASN ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 GLN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.140769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113723 restraints weight = 51247.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112594 restraints weight = 44247.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113339 restraints weight = 48736.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113980 restraints weight = 29611.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114932 restraints weight = 25508.330| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24372 Z= 0.124 Angle : 0.595 12.069 33308 Z= 0.307 Chirality : 0.041 0.160 3928 Planarity : 0.004 0.041 4248 Dihedral : 4.459 15.952 3456 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.40 % Allowed : 21.60 % Favored : 76.00 % 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: -0.05 (0.15), residues: 3220 helix: 0.95 (0.12), residues: 1836 sheet: -1.71 (0.34), residues: 180 loop : -1.26 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 333 TYR 0.019 0.001 TYR C 344 PHE 0.021 0.001 PHE H 68 TRP 0.013 0.001 TRP C 222 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00276 (24372) covalent geometry : angle 0.59540 (33308) hydrogen bonds : bond 0.03423 ( 1512) hydrogen bonds : angle 4.44442 ( 4332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 347 TYR cc_start: 0.6526 (m-80) cc_final: 0.6287 (t80) REVERT: A 487 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 139 GLU cc_start: 0.7896 (tp30) cc_final: 0.7693 (tp30) REVERT: D 123 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7905 (tm-30) REVERT: H 123 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 487 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7922 (tm-30) REVERT: E 109 PHE cc_start: 0.7942 (m-80) cc_final: 0.7708 (m-10) REVERT: E 458 MET cc_start: 0.8253 (tpp) cc_final: 0.7965 (tpp) REVERT: E 487 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7933 (tm-30) REVERT: E 530 GLN cc_start: 0.7804 (mp10) cc_final: 0.7540 (mp10) REVERT: G 109 PHE cc_start: 0.7957 (m-80) cc_final: 0.7711 (m-10) REVERT: G 487 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7904 (tm-30) outliers start: 53 outliers final: 26 residues processed: 383 average time/residue: 0.1220 time to fit residues: 80.4572 Evaluate side-chains 339 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 313 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 483 ASN Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 245 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN E 470 ASN E 545 ASN G 545 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103652 restraints weight = 51862.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105855 restraints weight = 29264.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107126 restraints weight = 21004.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107669 restraints weight = 17602.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107669 restraints weight = 16174.511| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24372 Z= 0.143 Angle : 0.602 11.971 33308 Z= 0.306 Chirality : 0.041 0.218 3928 Planarity : 0.004 0.041 4248 Dihedral : 4.329 17.503 3456 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.08 % Allowed : 23.14 % Favored : 74.77 % 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: 0.15 (0.15), residues: 3220 helix: 1.12 (0.12), residues: 1836 sheet: -1.65 (0.34), residues: 180 loop : -1.18 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 484 TYR 0.019 0.001 TYR E 230 PHE 0.027 0.001 PHE A 109 TRP 0.013 0.001 TRP A 222 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00324 (24372) covalent geometry : angle 0.60189 (33308) hydrogen bonds : bond 0.03344 ( 1512) hydrogen bonds : angle 4.36554 ( 4332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 347 TYR cc_start: 0.6515 (m-80) cc_final: 0.6289 (t80) REVERT: A 487 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 139 GLU cc_start: 0.7981 (tp30) cc_final: 0.7773 (tp30) REVERT: D 123 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7942 (tm-30) REVERT: H 123 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7700 (tm-30) REVERT: H 131 ASP cc_start: 0.8441 (p0) cc_final: 0.7834 (p0) REVERT: C 458 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7982 (tpp) REVERT: C 487 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7930 (tm-30) REVERT: E 109 PHE cc_start: 0.8159 (m-80) cc_final: 0.7956 (m-10) REVERT: E 487 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8040 (tm-30) REVERT: E 530 GLN cc_start: 0.7814 (mp10) cc_final: 0.7522 (mp10) REVERT: G 109 PHE cc_start: 0.8164 (m-80) cc_final: 0.7942 (m-10) REVERT: G 487 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 46 outliers final: 37 residues processed: 360 average time/residue: 0.1255 time to fit residues: 77.4934 Evaluate side-chains 346 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 441 ASN Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 441 ASN Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 237 optimal weight: 0.9980 chunk 205 optimal weight: 0.0010 chunk 238 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN G 470 ASN G 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105360 restraints weight = 51960.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107563 restraints weight = 28847.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108889 restraints weight = 20626.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109450 restraints weight = 17116.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109968 restraints weight = 15714.972| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24372 Z= 0.121 Angle : 0.575 10.309 33308 Z= 0.296 Chirality : 0.041 0.209 3928 Planarity : 0.003 0.040 4248 Dihedral : 4.198 17.690 3456 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.40 % Allowed : 23.73 % Favored : 73.87 % 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: 0.34 (0.15), residues: 3220 helix: 1.29 (0.12), residues: 1836 sheet: -1.42 (0.35), residues: 180 loop : -1.16 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 333 TYR 0.017 0.001 TYR E 230 PHE 0.026 0.001 PHE H 68 TRP 0.022 0.001 TRP C 365 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00270 (24372) covalent geometry : angle 0.57486 (33308) hydrogen bonds : bond 0.03179 ( 1512) hydrogen bonds : angle 4.25894 ( 4332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.8975 (mmt) cc_final: 0.8736 (mmt) REVERT: A 487 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 139 GLU cc_start: 0.7944 (tp30) cc_final: 0.7742 (tp30) REVERT: D 123 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7960 (tm-30) REVERT: F 123 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8024 (tm-30) REVERT: H 123 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7754 (tm-30) REVERT: H 131 ASP cc_start: 0.8438 (p0) cc_final: 0.7784 (p0) REVERT: C 458 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7799 (tpp) REVERT: C 487 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7930 (tm-30) REVERT: E 109 PHE cc_start: 0.8150 (m-80) cc_final: 0.7923 (m-10) REVERT: E 487 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 530 GLN cc_start: 0.7787 (mp10) cc_final: 0.7521 (mp10) REVERT: G 109 PHE cc_start: 0.8173 (m-80) cc_final: 0.7962 (m-10) REVERT: G 431 MET cc_start: 0.9220 (tpp) cc_final: 0.8669 (mmt) REVERT: G 458 MET cc_start: 0.8259 (tpp) cc_final: 0.8051 (tpp) REVERT: G 487 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7923 (tm-30) outliers start: 53 outliers final: 40 residues processed: 372 average time/residue: 0.1269 time to fit residues: 80.9727 Evaluate side-chains 365 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 212 HIS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 648 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 270 optimal weight: 30.0000 chunk 220 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 301 optimal weight: 0.7980 chunk 221 optimal weight: 0.0980 chunk 204 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114182 restraints weight = 51271.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112895 restraints weight = 44808.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113779 restraints weight = 49888.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114574 restraints weight = 29618.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115266 restraints weight = 25346.140| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24372 Z= 0.136 Angle : 0.601 16.269 33308 Z= 0.305 Chirality : 0.041 0.269 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.127 18.266 3456 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 24.41 % Favored : 73.37 % 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: 0.51 (0.15), residues: 3220 helix: 1.42 (0.12), residues: 1840 sheet: -1.31 (0.35), residues: 180 loop : -1.08 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 336 TYR 0.027 0.001 TYR E 230 PHE 0.025 0.001 PHE C 109 TRP 0.026 0.001 TRP E 365 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00312 (24372) covalent geometry : angle 0.60138 (33308) hydrogen bonds : bond 0.03187 ( 1512) hydrogen bonds : angle 4.22335 ( 4332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 341 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9089 (mmt) cc_final: 0.8762 (mmt) REVERT: A 487 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 139 GLU cc_start: 0.8026 (tp30) cc_final: 0.7777 (tp30) REVERT: D 123 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7937 (tm-30) REVERT: F 123 GLU cc_start: 0.8224 (tm-30) cc_final: 0.8016 (tm-30) REVERT: H 123 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7830 (tm-30) REVERT: H 131 ASP cc_start: 0.8567 (p0) cc_final: 0.7806 (p0) REVERT: C 487 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7856 (tm-30) REVERT: E 456 ILE cc_start: 0.9024 (tp) cc_final: 0.8620 (tp) REVERT: E 487 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 530 GLN cc_start: 0.7728 (mp10) cc_final: 0.7468 (mp10) REVERT: G 458 MET cc_start: 0.8459 (tpp) cc_final: 0.8173 (tpp) REVERT: G 487 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7857 (tm-30) outliers start: 49 outliers final: 34 residues processed: 376 average time/residue: 0.1231 time to fit residues: 80.0994 Evaluate side-chains 358 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 292 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 281 optimal weight: 0.5980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108081 restraints weight = 51324.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108843 restraints weight = 31372.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109486 restraints weight = 21660.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109547 restraints weight = 19877.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109532 restraints weight = 18767.138| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24372 Z= 0.139 Angle : 0.606 11.147 33308 Z= 0.309 Chirality : 0.041 0.263 3928 Planarity : 0.003 0.038 4248 Dihedral : 4.126 20.152 3456 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.86 % Allowed : 25.36 % Favored : 72.78 % 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: 0.58 (0.15), residues: 3220 helix: 1.47 (0.12), residues: 1848 sheet: -1.18 (0.36), residues: 180 loop : -1.08 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 336 TYR 0.027 0.001 TYR E 230 PHE 0.027 0.001 PHE H 68 TRP 0.029 0.002 TRP E 365 HIS 0.005 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00320 (24372) covalent geometry : angle 0.60590 (33308) hydrogen bonds : bond 0.03150 ( 1512) hydrogen bonds : angle 4.22331 ( 4332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7425 (t0) cc_final: 0.7202 (t0) REVERT: A 487 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 139 GLU cc_start: 0.8074 (tp30) cc_final: 0.7821 (tp30) REVERT: D 123 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7990 (tm-30) REVERT: F 123 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8051 (tm-30) REVERT: H 123 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7910 (tm-30) REVERT: H 131 ASP cc_start: 0.8615 (p0) cc_final: 0.7863 (p0) REVERT: C 99 MET cc_start: 0.8132 (tpp) cc_final: 0.7758 (tpp) REVERT: C 126 PHE cc_start: 0.8579 (m-10) cc_final: 0.8347 (m-10) REVERT: C 487 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 456 ILE cc_start: 0.9109 (tp) cc_final: 0.8737 (tp) REVERT: E 487 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7945 (tm-30) REVERT: E 530 GLN cc_start: 0.7809 (mp10) cc_final: 0.7534 (mp10) REVERT: G 487 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7900 (tm-30) outliers start: 41 outliers final: 35 residues processed: 371 average time/residue: 0.1247 time to fit residues: 80.5205 Evaluate side-chains 364 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 329 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 648 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 114 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.142107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110079 restraints weight = 51014.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109637 restraints weight = 32989.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110106 restraints weight = 26302.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110322 restraints weight = 24749.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110523 restraints weight = 22508.546| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24372 Z= 0.151 Angle : 0.623 14.155 33308 Z= 0.318 Chirality : 0.042 0.279 3928 Planarity : 0.003 0.038 4248 Dihedral : 4.143 19.823 3456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.68 % Allowed : 26.00 % Favored : 72.33 % 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: 0.61 (0.15), residues: 3220 helix: 1.50 (0.12), residues: 1848 sheet: -1.16 (0.36), residues: 180 loop : -1.08 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 336 TYR 0.027 0.001 TYR E 230 PHE 0.040 0.001 PHE E 109 TRP 0.029 0.002 TRP G 365 HIS 0.005 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00348 (24372) covalent geometry : angle 0.62266 (33308) hydrogen bonds : bond 0.03205 ( 1512) hydrogen bonds : angle 4.23585 ( 4332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3546.92 seconds wall clock time: 62 minutes 5.85 seconds (3725.85 seconds total)