Starting phenix.real_space_refine on Sun Jul 5 01:07:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.map" model { file = "/net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t22_25609/07_2026/7t22_25609.cif" } resolution = 4.2 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: 8 Type Number sf(0) Gaussians Al 5 5.89 5 P 23 5.49 5 Mg 5 5.21 5 S 99 5.16 5 C 15138 2.51 5 N 4323 2.21 5 O 4923 1.98 5 F 20 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24536 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "H" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "M" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.60, per 1000 atoms: 0.23 Number of scatterers: 24536 At special positions: 0 Unit cell: (161.68, 155.1, 152.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 99 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 4923 8.00 N 4323 7.00 C 15138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS G 568 " distance=2.04 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS H 568 " distance=2.04 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS I 568 " distance=2.04 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 911.4 milliseconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 7 sheets defined 66.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.540A pdb=" N ARG A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.586A pdb=" N THR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 Processing helix chain 'A' and resid 153 through 172 removed outlier: 3.528A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.561A pdb=" N GLN A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.725A pdb=" N ALA A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.504A pdb=" N LEU A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.776A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.705A pdb=" N ARG B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.596A pdb=" N TYR B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 Processing helix chain 'B' and resid 153 through 177 removed outlier: 3.585A pdb=" N ILE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 404 through 412 removed outlier: 4.700A pdb=" N ILE B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.735A pdb=" N TYR B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.580A pdb=" N GLY C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.691A pdb=" N TYR C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 182 through 199 removed outlier: 3.702A pdb=" N GLN C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.638A pdb=" N LEU C 402 " --> pdb=" O ASN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 412 removed outlier: 4.576A pdb=" N ILE C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.704A pdb=" N TYR C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.935A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 Processing helix chain 'D' and resid 153 through 172 removed outlier: 3.810A pdb=" N ARG D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 182 through 199 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 290 through 308 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 350 through 354 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.557A pdb=" N LEU D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 412 removed outlier: 4.324A pdb=" N ILE D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.912A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 47 through 53 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.622A pdb=" N TYR E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 Processing helix chain 'E' and resid 153 through 172 removed outlier: 3.646A pdb=" N ARG E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 199 removed outlier: 4.182A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 290 through 308 Processing helix chain 'E' and resid 319 through 335 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 350 through 354 Processing helix chain 'E' and resid 356 through 376 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.697A pdb=" N LEU E 402 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 removed outlier: 4.377A pdb=" N ILE E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.895A pdb=" N TYR E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.926A pdb=" N ARG F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.689A pdb=" N TYR F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 118 through 148 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.968A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 182 through 198 removed outlier: 4.310A pdb=" N PHE F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 236 through 251 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 290 through 308 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 350 through 354 Processing helix chain 'F' and resid 356 through 376 Processing helix chain 'F' and resid 387 through 392 removed outlier: 3.706A pdb=" N GLN F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 387 through 392' Processing helix chain 'F' and resid 398 through 402 Processing helix chain 'F' and resid 404 through 412 removed outlier: 3.645A pdb=" N ILE F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.737A pdb=" N TYR F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.603A pdb=" N THR G 466 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 495 removed outlier: 3.780A pdb=" N GLN G 495 " --> pdb=" O THR G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 506 through 511 removed outlier: 4.599A pdb=" N GLY G 509 " --> pdb=" O HIS G 506 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN G 511 " --> pdb=" O ARG G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 522 removed outlier: 3.646A pdb=" N MET G 521 " --> pdb=" O GLU G 517 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP G 522 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 559 removed outlier: 3.601A pdb=" N GLU G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN G 533 " --> pdb=" O ASN G 529 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU G 553 " --> pdb=" O LEU G 549 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG G 559 " --> pdb=" O ILE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 580 removed outlier: 3.587A pdb=" N LEU G 574 " --> pdb=" O GLU G 570 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN G 576 " --> pdb=" O TRP G 572 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 577 " --> pdb=" O THR G 573 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 578 " --> pdb=" O LEU G 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 461 Processing helix chain 'H' and resid 462 through 468 removed outlier: 3.821A pdb=" N THR H 466 " --> pdb=" O GLU H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 493 removed outlier: 4.381A pdb=" N PHE H 485 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 505 Processing helix chain 'H' and resid 506 through 508 No H-bonds generated for 'chain 'H' and resid 506 through 508' Processing helix chain 'H' and resid 512 through 522 removed outlier: 3.759A pdb=" N MET H 521 " --> pdb=" O GLU H 517 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 562 removed outlier: 3.815A pdb=" N THR H 534 " --> pdb=" O ILE H 530 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 546 " --> pdb=" O MET H 542 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 547 " --> pdb=" O PHE H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 580 removed outlier: 3.589A pdb=" N LEU H 578 " --> pdb=" O LEU H 574 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 580 " --> pdb=" O GLN H 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 462 through 468 Processing helix chain 'I' and resid 481 through 495 removed outlier: 4.395A pdb=" N PHE I 485 " --> pdb=" O GLY I 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN I 495 " --> pdb=" O THR I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 505 Processing helix chain 'I' and resid 506 through 511 removed outlier: 4.575A pdb=" N GLY I 509 " --> pdb=" O HIS I 506 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASN I 511 " --> pdb=" O ARG I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 522 removed outlier: 3.632A pdb=" N MET I 521 " --> pdb=" O GLU I 517 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP I 522 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 562 removed outlier: 3.850A pdb=" N GLU I 532 " --> pdb=" O LYS I 528 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN I 533 " --> pdb=" O ASN I 529 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR I 534 " --> pdb=" O ILE I 530 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 545 " --> pdb=" O HIS I 541 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU I 546 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU I 547 " --> pdb=" O PHE I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 580 removed outlier: 3.642A pdb=" N GLU I 577 " --> pdb=" O THR I 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 578 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 579 " --> pdb=" O ASN I 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS I 580 " --> pdb=" O GLN I 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.420A pdb=" N LEU B 257 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP B 343 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE B 259 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 384 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 227 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 383 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 229 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.059A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 414 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 227 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER A 383 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 229 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 340 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU A 382 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 342 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLN A 384 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP A 313 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 258 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 181 removed outlier: 6.358A pdb=" N VAL C 256 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP C 313 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 257 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP C 343 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C 259 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 340 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU C 382 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 342 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 227 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER C 383 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 229 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 226 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET C 416 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 180 through 181 removed outlier: 6.599A pdb=" N LEU D 257 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP D 343 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE D 259 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE D 340 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D 382 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 342 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 227 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER D 383 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 229 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.246A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP E 343 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 259 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 227 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER E 383 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 229 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.246A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP E 343 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 259 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 227 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU E 226 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N MET E 416 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 228 " --> pdb=" O MET E 416 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE E 418 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 230 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 310 through 313 removed outlier: 6.418A pdb=" N VAL F 256 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP F 313 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 258 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 229 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 231 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) 1468 hydrogen bonds defined for protein. 4128 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: 4.55 Time building geometry restraints manager: 2.80 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: 8476 1.34 - 1.46: 4408 1.46 - 1.58: 11770 1.58 - 1.70: 40 1.70 - 1.82: 206 Bond restraints: 24900 Sorted by residual: bond pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.684 1.805 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F4 ALF C1002 " pdb="AL ALF C1002 " ideal model delta sigma weight residual 1.686 1.804 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 24895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.09: 33747 14.09 - 28.19: 20 28.19 - 42.28: 0 42.28 - 56.37: 0 56.37 - 70.46: 10 Bond angle restraints: 33777 Sorted by residual: angle pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " pdb=" F2 ALF E1002 " ideal model delta sigma weight residual 108.68 179.14 -70.46 3.00e+00 1.11e-01 5.52e+02 angle pdb=" F1 ALF C1002 " pdb="AL ALF C1002 " pdb=" F2 ALF C1002 " ideal model delta sigma weight residual 108.68 179.11 -70.43 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " pdb=" F2 ALF D1002 " ideal model delta sigma weight residual 108.68 179.08 -70.40 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " pdb=" F2 ALF B1002 " ideal model delta sigma weight residual 108.68 179.03 -70.35 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " pdb=" F2 ALF F1002 " ideal model delta sigma weight residual 108.68 178.95 -70.27 3.00e+00 1.11e-01 5.49e+02 ... (remaining 33772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 15164 30.03 - 60.06: 166 60.06 - 90.09: 6 90.09 - 120.12: 7 120.12 - 150.15: 1 Dihedral angle restraints: 15344 sinusoidal: 6416 harmonic: 8928 Sorted by residual: dihedral pdb=" CA GLU D 404 " pdb=" C GLU D 404 " pdb=" N SER D 405 " pdb=" CA SER D 405 " ideal model delta harmonic sigma weight residual 180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 90.15 -150.15 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" CA GLU E 404 " pdb=" C GLU E 404 " pdb=" N SER E 405 " pdb=" CA SER E 405 " ideal model delta harmonic sigma weight residual -180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 15341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2909 0.034 - 0.067: 590 0.067 - 0.101: 199 0.101 - 0.134: 139 0.134 - 0.168: 15 Chirality restraints: 3852 Sorted by residual: chirality pdb=" C3' DT M 8 " pdb=" C4' DT M 8 " pdb=" O3' DT M 8 " pdb=" C2' DT M 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" C3' DT M 9 " pdb=" C4' DT M 9 " pdb=" O3' DT M 9 " pdb=" C2' DT M 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C3' DT M 7 " pdb=" C4' DT M 7 " pdb=" O3' DT M 7 " pdb=" C2' DT M 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 3849 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 199 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO F 200 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 199 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 200 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 468 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO G 469 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 469 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 469 " 0.015 5.00e-02 4.00e+02 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 327 2.57 - 3.15: 21509 3.15 - 3.74: 40104 3.74 - 4.32: 53707 4.32 - 4.90: 90437 Nonbonded interactions: 206084 Sorted by model distance: nonbonded pdb=" F4 ALF F1002 " pdb="MG MG F1003 " model vdw 1.992 2.120 nonbonded pdb=" F4 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F4 ALF D1002 " pdb="MG MG D1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF F1002 " pdb="MG MG F1003 " model vdw 1.994 2.120 ... (remaining 206079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 24 through 471) selection = (chain 'C' and resid 24 through 471) selection = (chain 'D' and resid 24 through 471) selection = (chain 'E' and resid 24 through 471) selection = (chain 'F' and resid 24 through 471) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.220 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.255 24908 Z= 0.422 Angle : 1.415 70.464 33783 Z= 0.547 Chirality : 0.038 0.168 3852 Planarity : 0.003 0.038 4422 Dihedral : 10.318 150.151 9545 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 3.45 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.16), residues: 3066 helix: 2.89 (0.13), residues: 1717 sheet: -0.92 (0.26), residues: 319 loop : 0.48 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 387 TYR 0.008 0.001 TYR B 344 PHE 0.006 0.001 PHE D 166 TRP 0.006 0.001 TRP B 48 HIS 0.003 0.001 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 (24900) covalent geometry : angle 1.41521 / 0.55 (33777) SS BOND : bond 0.00543 / 0.27 ( 3) SS BOND : angle 1.24451 / 0.57 ( 6) hydrogen bonds : bond 0.15030 / 10.68 ( 1466) hydrogen bonds : angle 4.78735 / 3.48 ( 4128) Misc. bond : bond 0.25360 / 13.95 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 659 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8368 (tt0) cc_final: 0.8072 (pp20) REVERT: A 58 ASP cc_start: 0.9083 (m-30) cc_final: 0.8654 (p0) REVERT: A 135 MET cc_start: 0.9057 (ttm) cc_final: 0.8515 (ppp) REVERT: A 291 ASP cc_start: 0.8674 (m-30) cc_final: 0.8095 (p0) REVERT: A 345 LEU cc_start: 0.8307 (mt) cc_final: 0.7830 (mt) REVERT: B 72 MET cc_start: 0.8897 (mtt) cc_final: 0.8637 (mtt) REVERT: B 226 LEU cc_start: 0.8288 (tp) cc_final: 0.7775 (mm) REVERT: B 240 PHE cc_start: 0.9322 (t80) cc_final: 0.9079 (t80) REVERT: B 263 MET cc_start: 0.6032 (mtp) cc_final: 0.5786 (mtt) REVERT: B 269 MET cc_start: 0.8878 (tpp) cc_final: 0.8591 (tpp) REVERT: B 291 ASP cc_start: 0.8979 (m-30) cc_final: 0.8735 (p0) REVERT: B 324 ARG cc_start: 0.9166 (ttm170) cc_final: 0.8899 (ttm-80) REVERT: B 348 MET cc_start: 0.7184 (mtp) cc_final: 0.6966 (ttm) REVERT: B 414 LEU cc_start: 0.9277 (tp) cc_final: 0.8938 (tp) REVERT: C 60 PHE cc_start: 0.9225 (m-80) cc_final: 0.8921 (m-10) REVERT: C 61 TYR cc_start: 0.8669 (t80) cc_final: 0.8430 (t80) REVERT: C 240 PHE cc_start: 0.8919 (t80) cc_final: 0.8480 (t80) REVERT: C 259 PHE cc_start: 0.9023 (m-80) cc_final: 0.8749 (m-80) REVERT: C 263 MET cc_start: 0.7866 (mtp) cc_final: 0.7514 (ttm) REVERT: C 269 MET cc_start: 0.8870 (tpp) cc_final: 0.8559 (ttt) REVERT: C 270 MET cc_start: 0.9052 (mtm) cc_final: 0.8236 (mtp) REVERT: C 382 LEU cc_start: 0.8828 (mt) cc_final: 0.8326 (mt) REVERT: D 50 ASP cc_start: 0.8181 (m-30) cc_final: 0.7810 (p0) REVERT: D 58 ASP cc_start: 0.9006 (m-30) cc_final: 0.8762 (p0) REVERT: D 87 LEU cc_start: 0.8533 (tp) cc_final: 0.7932 (pp) REVERT: D 118 ASN cc_start: 0.9391 (m-40) cc_final: 0.9089 (m-40) REVERT: D 160 LEU cc_start: 0.9159 (tp) cc_final: 0.8873 (tt) REVERT: D 228 ILE cc_start: 0.8273 (mm) cc_final: 0.8044 (mm) REVERT: D 237 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8189 (ptpt) REVERT: D 263 MET cc_start: 0.8062 (mtp) cc_final: 0.7789 (mtt) REVERT: D 337 ILE cc_start: 0.8701 (mt) cc_final: 0.8411 (mm) REVERT: D 341 MET cc_start: 0.7657 (tmt) cc_final: 0.7042 (tmm) REVERT: D 363 GLU cc_start: 0.7849 (tp30) cc_final: 0.7256 (tm-30) REVERT: D 426 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7601 (tp30) REVERT: E 60 PHE cc_start: 0.8983 (m-80) cc_final: 0.8285 (m-80) REVERT: E 92 GLU cc_start: 0.8879 (tt0) cc_final: 0.8484 (tm-30) REVERT: E 135 MET cc_start: 0.9300 (ttm) cc_final: 0.8934 (tmm) REVERT: E 235 MET cc_start: 0.8937 (mmt) cc_final: 0.8143 (mmm) REVERT: E 270 MET cc_start: 0.8963 (mtm) cc_final: 0.8354 (ppp) REVERT: E 301 MET cc_start: 0.9056 (mtp) cc_final: 0.8105 (tpp) REVERT: E 310 ILE cc_start: 0.9285 (mt) cc_final: 0.8954 (mm) REVERT: E 320 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: E 363 GLU cc_start: 0.9103 (tp30) cc_final: 0.8898 (tp30) REVERT: E 443 ASN cc_start: 0.8521 (m-40) cc_final: 0.7423 (t0) REVERT: F 282 THR cc_start: 0.9096 (m) cc_final: 0.8803 (p) REVERT: F 361 ILE cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: F 414 LEU cc_start: 0.9094 (tp) cc_final: 0.8892 (tp) REVERT: G 471 LEU cc_start: 0.7256 (pp) cc_final: 0.6464 (mp) REVERT: G 521 MET cc_start: 0.9210 (ppp) cc_final: 0.9008 (ppp) REVERT: G 553 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: G 568 CYS cc_start: 0.8504 (m) cc_final: 0.8111 (t) REVERT: H 498 LEU cc_start: 0.0378 (pt) cc_final: -0.0328 (pt) REVERT: H 550 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8648 (mmm160) REVERT: I 530 ILE cc_start: 0.8998 (tt) cc_final: 0.8670 (pt) outliers start: 31 outliers final: 4 residues processed: 683 average time/residue: 0.1912 time to fit residues: 194.7973 Evaluate side-chains 377 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 372 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 76 GLN A 96 GLN A 410 GLN A 441 GLN B 45 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN E 181 ASN F 96 GLN F 243 ASN F 441 GLN G 541 HIS I 502 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.077648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.060572 restraints weight = 164293.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.062012 restraints weight = 116131.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.063045 restraints weight = 89481.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.063844 restraints weight = 73182.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.064419 restraints weight = 62448.931| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24908 Z= 0.185 Angle : 1.058 31.439 33783 Z= 0.434 Chirality : 0.043 0.236 3852 Planarity : 0.005 0.084 4422 Dihedral : 7.587 124.205 3554 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.34 % Allowed : 2.13 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.94 (0.15), residues: 3066 helix: 2.18 (0.12), residues: 1771 sheet: -0.58 (0.27), residues: 320 loop : 0.38 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 387 TYR 0.023 0.002 TYR F 122 PHE 0.029 0.002 PHE B 197 TRP 0.020 0.002 TRP A 48 HIS 0.008 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (24900) covalent geometry : angle 1.05781 / 0.43 (33777) SS BOND : bond 0.00646 / 0.33 ( 3) SS BOND : angle 1.71125 / 0.83 ( 6) hydrogen bonds : bond 0.04169 / 2.88 ( 1466) hydrogen bonds : angle 4.39769 / 3.19 ( 4128) Misc. bond : bond 0.00089 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 444 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9106 (m-30) cc_final: 0.8651 (p0) REVERT: A 194 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8951 (tp30) REVERT: A 291 ASP cc_start: 0.8807 (m-30) cc_final: 0.8249 (p0) REVERT: A 345 LEU cc_start: 0.8040 (mt) cc_final: 0.7756 (mt) REVERT: B 72 MET cc_start: 0.8652 (mtt) cc_final: 0.8384 (mtt) REVERT: B 226 LEU cc_start: 0.8424 (tp) cc_final: 0.8112 (mm) REVERT: B 240 PHE cc_start: 0.9189 (t80) cc_final: 0.8944 (t80) REVERT: B 269 MET cc_start: 0.8961 (tpp) cc_final: 0.8536 (tpp) REVERT: B 291 ASP cc_start: 0.8971 (m-30) cc_final: 0.8714 (p0) REVERT: B 297 ILE cc_start: 0.9475 (mm) cc_final: 0.9231 (pt) REVERT: B 301 MET cc_start: 0.8952 (tmm) cc_final: 0.8708 (tmm) REVERT: B 324 ARG cc_start: 0.9194 (ttm170) cc_final: 0.8705 (ttt180) REVERT: B 348 MET cc_start: 0.7359 (mtp) cc_final: 0.6811 (mpp) REVERT: B 414 LEU cc_start: 0.9161 (tp) cc_final: 0.8878 (tp) REVERT: C 235 MET cc_start: 0.9100 (mmp) cc_final: 0.8801 (mmm) REVERT: C 259 PHE cc_start: 0.9229 (m-80) cc_final: 0.8810 (m-80) REVERT: C 263 MET cc_start: 0.8361 (mtp) cc_final: 0.8097 (ttm) REVERT: C 269 MET cc_start: 0.8831 (tpp) cc_final: 0.8626 (ttt) REVERT: C 312 ILE cc_start: 0.9446 (mp) cc_final: 0.9032 (tt) REVERT: C 322 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 382 LEU cc_start: 0.8870 (mt) cc_final: 0.8626 (mt) REVERT: C 427 ASN cc_start: 0.8088 (p0) cc_final: 0.7747 (p0) REVERT: D 34 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8751 (mt-10) REVERT: D 58 ASP cc_start: 0.9041 (m-30) cc_final: 0.8788 (p0) REVERT: D 118 ASN cc_start: 0.9466 (m-40) cc_final: 0.9156 (m-40) REVERT: D 160 LEU cc_start: 0.9205 (tp) cc_final: 0.8907 (tt) REVERT: D 237 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8406 (ptpt) REVERT: D 269 MET cc_start: 0.8559 (ttm) cc_final: 0.8173 (ttm) REVERT: D 301 MET cc_start: 0.8894 (mtm) cc_final: 0.8522 (mtt) REVERT: D 337 ILE cc_start: 0.8701 (mt) cc_final: 0.8471 (mm) REVERT: E 60 PHE cc_start: 0.9132 (m-80) cc_final: 0.8910 (m-80) REVERT: E 85 ILE cc_start: 0.9535 (pt) cc_final: 0.9269 (mp) REVERT: E 92 GLU cc_start: 0.8821 (tt0) cc_final: 0.8572 (tm-30) REVERT: E 135 MET cc_start: 0.9268 (ttm) cc_final: 0.9047 (tmm) REVERT: E 235 MET cc_start: 0.8849 (mmt) cc_final: 0.7853 (mmm) REVERT: E 267 GLN cc_start: 0.9182 (mp10) cc_final: 0.8953 (mp10) REVERT: E 310 ILE cc_start: 0.9446 (mt) cc_final: 0.9182 (mm) REVERT: E 363 GLU cc_start: 0.9171 (tp30) cc_final: 0.8840 (tp30) REVERT: F 98 ASP cc_start: 0.7781 (t0) cc_final: 0.7568 (p0) REVERT: F 235 MET cc_start: 0.7357 (mtt) cc_final: 0.6494 (mtp) REVERT: F 263 MET cc_start: 0.7005 (mpp) cc_final: 0.6706 (mpp) REVERT: F 282 THR cc_start: 0.9215 (m) cc_final: 0.8905 (p) REVERT: F 318 LEU cc_start: 0.8401 (mp) cc_final: 0.8148 (mp) REVERT: G 468 VAL cc_start: 0.6705 (t) cc_final: 0.6359 (t) REVERT: G 568 CYS cc_start: 0.8133 (m) cc_final: 0.7724 (t) REVERT: H 541 HIS cc_start: 0.8780 (m90) cc_final: 0.8546 (m170) REVERT: H 550 ARG cc_start: 0.8963 (mmp80) cc_final: 0.8693 (mmm160) REVERT: I 489 VAL cc_start: 0.4240 (t) cc_final: 0.4017 (t) REVERT: I 530 ILE cc_start: 0.8876 (tt) cc_final: 0.8658 (pt) outliers start: 9 outliers final: 2 residues processed: 449 average time/residue: 0.1807 time to fit residues: 124.5549 Evaluate side-chains 317 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 12 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.076227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.059316 restraints weight = 170634.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.060760 restraints weight = 121522.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.061781 restraints weight = 93458.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.062557 restraints weight = 76482.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.063125 restraints weight = 65334.897| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24908 Z= 0.178 Angle : 1.034 30.601 33783 Z= 0.421 Chirality : 0.041 0.240 3852 Planarity : 0.005 0.092 4422 Dihedral : 7.395 126.071 3554 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.70 (0.15), residues: 3066 helix: 1.90 (0.12), residues: 1777 sheet: -0.45 (0.28), residues: 319 loop : 0.37 (0.22), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 328 TYR 0.025 0.002 TYR B 122 PHE 0.020 0.002 PHE F 240 TRP 0.021 0.002 TRP A 48 HIS 0.013 0.002 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (24900) covalent geometry : angle 1.03349 / 0.42 (33777) SS BOND : bond 0.00835 / 0.43 ( 3) SS BOND : angle 1.88035 / 0.96 ( 6) hydrogen bonds : bond 0.03739 / 2.59 ( 1466) hydrogen bonds : angle 4.38135 / 3.20 ( 4128) Misc. bond : bond 0.00179 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 410 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9140 (m-30) cc_final: 0.8673 (p0) REVERT: A 135 MET cc_start: 0.9085 (mmm) cc_final: 0.8872 (mmm) REVERT: A 194 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8997 (tp30) REVERT: A 242 MET cc_start: 0.8911 (ppp) cc_final: 0.8668 (ppp) REVERT: A 291 ASP cc_start: 0.8822 (m-30) cc_final: 0.8254 (p0) REVERT: A 345 LEU cc_start: 0.8006 (mt) cc_final: 0.7675 (mt) REVERT: A 348 MET cc_start: 0.9153 (ttm) cc_final: 0.8805 (ttm) REVERT: A 416 MET cc_start: 0.8627 (mmt) cc_final: 0.8086 (mmm) REVERT: A 438 ILE cc_start: 0.8394 (mp) cc_final: 0.7671 (mp) REVERT: B 72 MET cc_start: 0.8652 (mtt) cc_final: 0.8450 (mtt) REVERT: B 226 LEU cc_start: 0.8205 (tp) cc_final: 0.7793 (mm) REVERT: B 235 MET cc_start: 0.8329 (mmp) cc_final: 0.8045 (mmm) REVERT: B 240 PHE cc_start: 0.9109 (t80) cc_final: 0.8884 (t80) REVERT: B 269 MET cc_start: 0.9038 (tpp) cc_final: 0.8661 (tpp) REVERT: B 291 ASP cc_start: 0.8952 (m-30) cc_final: 0.8708 (p0) REVERT: B 297 ILE cc_start: 0.9446 (mm) cc_final: 0.9210 (pt) REVERT: B 301 MET cc_start: 0.9032 (tmm) cc_final: 0.8766 (tmm) REVERT: B 324 ARG cc_start: 0.9177 (ttm170) cc_final: 0.8638 (ttt180) REVERT: B 348 MET cc_start: 0.7464 (mtp) cc_final: 0.7130 (ttm) REVERT: C 235 MET cc_start: 0.9002 (mmp) cc_final: 0.8716 (mmm) REVERT: C 259 PHE cc_start: 0.9134 (m-80) cc_final: 0.8810 (m-80) REVERT: C 263 MET cc_start: 0.8474 (mtp) cc_final: 0.8187 (ttm) REVERT: C 322 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8195 (mt-10) REVERT: C 382 LEU cc_start: 0.8844 (mt) cc_final: 0.8335 (mt) REVERT: C 419 TYR cc_start: 0.7770 (t80) cc_final: 0.7498 (t80) REVERT: C 427 ASN cc_start: 0.8143 (p0) cc_final: 0.7858 (p0) REVERT: D 58 ASP cc_start: 0.9054 (m-30) cc_final: 0.8811 (p0) REVERT: D 118 ASN cc_start: 0.9484 (m-40) cc_final: 0.9239 (m-40) REVERT: D 160 LEU cc_start: 0.9244 (tp) cc_final: 0.8944 (tt) REVERT: D 284 ILE cc_start: 0.9195 (mt) cc_final: 0.8992 (mt) REVERT: D 301 MET cc_start: 0.8906 (mtm) cc_final: 0.8590 (mtt) REVERT: D 337 ILE cc_start: 0.8668 (mt) cc_final: 0.8451 (mm) REVERT: E 42 MET cc_start: 0.8370 (mtm) cc_final: 0.7965 (ptp) REVERT: E 92 GLU cc_start: 0.8787 (tt0) cc_final: 0.8445 (tm-30) REVERT: E 135 MET cc_start: 0.9290 (ttm) cc_final: 0.9045 (tmm) REVERT: E 235 MET cc_start: 0.8899 (mmt) cc_final: 0.8000 (mmm) REVERT: E 363 GLU cc_start: 0.9173 (tp30) cc_final: 0.8851 (tp30) REVERT: F 98 ASP cc_start: 0.7798 (t0) cc_final: 0.7555 (p0) REVERT: F 270 MET cc_start: 0.8207 (ttt) cc_final: 0.7923 (ttt) REVERT: F 282 THR cc_start: 0.9244 (m) cc_final: 0.8901 (p) REVERT: F 391 GLN cc_start: 0.9381 (mt0) cc_final: 0.9159 (mt0) REVERT: G 537 ASP cc_start: 0.8773 (t0) cc_final: 0.8442 (t0) REVERT: G 568 CYS cc_start: 0.8031 (m) cc_final: 0.7675 (t) REVERT: H 541 HIS cc_start: 0.8897 (m90) cc_final: 0.8665 (m170) REVERT: H 550 ARG cc_start: 0.8976 (mmp80) cc_final: 0.8697 (mmm160) REVERT: I 489 VAL cc_start: 0.4261 (t) cc_final: 0.4048 (t) REVERT: I 530 ILE cc_start: 0.8941 (tt) cc_final: 0.8713 (pt) outliers start: 2 outliers final: 0 residues processed: 411 average time/residue: 0.1769 time to fit residues: 113.3324 Evaluate side-chains 313 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 28 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 195 GLN B 281 GLN D 45 ASN F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.075603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.058936 restraints weight = 169767.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.060244 restraints weight = 122771.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.061193 restraints weight = 95982.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.061893 restraints weight = 79552.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.062438 restraints weight = 68794.134| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24908 Z= 0.166 Angle : 1.023 30.477 33783 Z= 0.413 Chirality : 0.041 0.173 3852 Planarity : 0.004 0.069 4422 Dihedral : 7.202 127.436 3554 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.59 (0.15), residues: 3066 helix: 1.80 (0.12), residues: 1792 sheet: -0.45 (0.28), residues: 318 loop : 0.31 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 442 TYR 0.029 0.002 TYR B 122 PHE 0.017 0.002 PHE F 240 TRP 0.024 0.001 TRP A 48 HIS 0.007 0.001 HIS G 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (24900) covalent geometry : angle 1.02265 / 0.41 (33777) SS BOND : bond 0.00929 / 0.48 ( 3) SS BOND : angle 1.63750 / 0.78 ( 6) hydrogen bonds : bond 0.03448 / 2.39 ( 1466) hydrogen bonds : angle 4.33832 / 3.17 ( 4128) Misc. bond : bond 0.00169 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9191 (m-30) cc_final: 0.8690 (p0) REVERT: A 135 MET cc_start: 0.9076 (mmm) cc_final: 0.8861 (mmm) REVERT: A 194 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8944 (tp30) REVERT: A 242 MET cc_start: 0.8912 (ppp) cc_final: 0.8598 (ppp) REVERT: A 291 ASP cc_start: 0.8802 (m-30) cc_final: 0.8214 (p0) REVERT: A 345 LEU cc_start: 0.7957 (mt) cc_final: 0.7588 (mt) REVERT: A 416 MET cc_start: 0.8651 (mmt) cc_final: 0.8111 (mmm) REVERT: A 438 ILE cc_start: 0.8262 (mp) cc_final: 0.7606 (mp) REVERT: B 72 MET cc_start: 0.8760 (mtt) cc_final: 0.8478 (mtt) REVERT: B 240 PHE cc_start: 0.9078 (t80) cc_final: 0.8831 (t80) REVERT: B 269 MET cc_start: 0.9027 (tpp) cc_final: 0.8633 (tpp) REVERT: B 291 ASP cc_start: 0.8902 (m-30) cc_final: 0.8648 (p0) REVERT: B 297 ILE cc_start: 0.9417 (mm) cc_final: 0.9185 (pt) REVERT: B 301 MET cc_start: 0.9040 (tmm) cc_final: 0.8721 (tmm) REVERT: B 324 ARG cc_start: 0.9115 (ttm170) cc_final: 0.8605 (ttt180) REVERT: B 348 MET cc_start: 0.7495 (mtp) cc_final: 0.7103 (ttm) REVERT: C 51 VAL cc_start: 0.8393 (t) cc_final: 0.8167 (p) REVERT: C 235 MET cc_start: 0.9003 (mmp) cc_final: 0.8695 (mmm) REVERT: C 259 PHE cc_start: 0.9125 (m-80) cc_final: 0.8885 (m-80) REVERT: C 312 ILE cc_start: 0.9474 (mp) cc_final: 0.9105 (tt) REVERT: C 322 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8111 (mt-10) REVERT: C 382 LEU cc_start: 0.8869 (mt) cc_final: 0.8452 (mt) REVERT: C 419 TYR cc_start: 0.7725 (t80) cc_final: 0.7329 (t80) REVERT: C 427 ASN cc_start: 0.8121 (p0) cc_final: 0.7857 (p0) REVERT: D 42 MET cc_start: 0.7446 (mtp) cc_final: 0.7089 (mtp) REVERT: D 118 ASN cc_start: 0.9497 (m-40) cc_final: 0.9180 (m-40) REVERT: D 160 LEU cc_start: 0.9259 (tp) cc_final: 0.8956 (tt) REVERT: D 235 MET cc_start: 0.8964 (mmp) cc_final: 0.8760 (mmp) REVERT: D 301 MET cc_start: 0.8921 (mtm) cc_final: 0.8563 (mtt) REVERT: E 42 MET cc_start: 0.8350 (mtm) cc_final: 0.7955 (ptp) REVERT: E 92 GLU cc_start: 0.8758 (tt0) cc_final: 0.8432 (tm-30) REVERT: E 135 MET cc_start: 0.9231 (ttm) cc_final: 0.9019 (tmm) REVERT: E 235 MET cc_start: 0.8848 (mmt) cc_final: 0.8028 (mmm) REVERT: E 301 MET cc_start: 0.9106 (mtm) cc_final: 0.8770 (mtt) REVERT: E 348 MET cc_start: 0.8425 (mmp) cc_final: 0.8047 (mmp) REVERT: E 363 GLU cc_start: 0.9140 (tp30) cc_final: 0.8831 (tp30) REVERT: F 98 ASP cc_start: 0.7804 (t0) cc_final: 0.7558 (p0) REVERT: F 235 MET cc_start: 0.7414 (mtt) cc_final: 0.6510 (mtp) REVERT: F 263 MET cc_start: 0.6798 (mpp) cc_final: 0.6558 (mpp) REVERT: F 270 MET cc_start: 0.8524 (ttt) cc_final: 0.8242 (ttt) REVERT: F 391 GLN cc_start: 0.9420 (mt0) cc_final: 0.9153 (mt0) REVERT: G 512 ASN cc_start: 0.7861 (t0) cc_final: 0.6732 (m110) REVERT: G 537 ASP cc_start: 0.8753 (t0) cc_final: 0.8421 (t0) REVERT: G 568 CYS cc_start: 0.8146 (m) cc_final: 0.7740 (t) REVERT: H 541 HIS cc_start: 0.8947 (m90) cc_final: 0.8726 (m170) REVERT: H 550 ARG cc_start: 0.9003 (mmp80) cc_final: 0.8714 (mmm160) REVERT: I 489 VAL cc_start: 0.3974 (t) cc_final: 0.3757 (t) REVERT: I 530 ILE cc_start: 0.8910 (tt) cc_final: 0.8687 (pt) outliers start: 2 outliers final: 2 residues processed: 397 average time/residue: 0.1778 time to fit residues: 110.1345 Evaluate side-chains 299 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 0.7980 chunk 282 optimal weight: 7.9990 chunk 299 optimal weight: 40.0000 chunk 291 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.074122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.057568 restraints weight = 172274.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.058879 restraints weight = 125077.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.059833 restraints weight = 97874.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.060480 restraints weight = 81004.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.061032 restraints weight = 70223.611| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24908 Z= 0.179 Angle : 1.028 31.219 33783 Z= 0.416 Chirality : 0.041 0.163 3852 Planarity : 0.004 0.058 4422 Dihedral : 7.083 130.648 3554 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.49 (0.15), residues: 3066 helix: 1.73 (0.12), residues: 1787 sheet: -0.57 (0.28), residues: 317 loop : 0.29 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 387 TYR 0.025 0.002 TYR D 122 PHE 0.015 0.002 PHE F 240 TRP 0.024 0.002 TRP A 48 HIS 0.006 0.001 HIS G 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (24900) covalent geometry : angle 1.02785 / 0.42 (33777) SS BOND : bond 0.01001 / 0.52 ( 3) SS BOND : angle 2.02625 / 1.05 ( 6) hydrogen bonds : bond 0.03372 / 2.32 ( 1466) hydrogen bonds : angle 4.41094 / 3.23 ( 4128) Misc. bond : bond 0.00175 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9200 (m-30) cc_final: 0.8695 (p0) REVERT: A 135 MET cc_start: 0.9118 (mmm) cc_final: 0.8900 (mmm) REVERT: A 194 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8957 (tp30) REVERT: A 291 ASP cc_start: 0.8831 (m-30) cc_final: 0.8215 (p0) REVERT: A 345 LEU cc_start: 0.7935 (mt) cc_final: 0.7578 (mt) REVERT: A 416 MET cc_start: 0.8686 (mmt) cc_final: 0.8092 (mmm) REVERT: A 438 ILE cc_start: 0.8207 (mp) cc_final: 0.7528 (mp) REVERT: B 42 MET cc_start: 0.8181 (mtm) cc_final: 0.7582 (ttm) REVERT: B 72 MET cc_start: 0.8745 (mtt) cc_final: 0.8533 (mtt) REVERT: B 235 MET cc_start: 0.8516 (mmp) cc_final: 0.8135 (mmm) REVERT: B 240 PHE cc_start: 0.9096 (t80) cc_final: 0.8826 (t80) REVERT: B 269 MET cc_start: 0.8973 (tpp) cc_final: 0.8568 (tpp) REVERT: B 291 ASP cc_start: 0.8942 (m-30) cc_final: 0.8684 (p0) REVERT: B 297 ILE cc_start: 0.9423 (mm) cc_final: 0.9203 (pt) REVERT: B 301 MET cc_start: 0.9064 (tmm) cc_final: 0.8730 (tmm) REVERT: B 348 MET cc_start: 0.7636 (mtp) cc_final: 0.7181 (ttm) REVERT: B 364 ILE cc_start: 0.8767 (mt) cc_final: 0.8561 (mt) REVERT: B 414 LEU cc_start: 0.9203 (tp) cc_final: 0.8746 (tt) REVERT: C 235 MET cc_start: 0.9035 (mmp) cc_final: 0.8744 (mmm) REVERT: C 312 ILE cc_start: 0.9491 (mp) cc_final: 0.9075 (tt) REVERT: C 322 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 382 LEU cc_start: 0.8871 (mt) cc_final: 0.8644 (mt) REVERT: C 419 TYR cc_start: 0.7664 (t80) cc_final: 0.7166 (t80) REVERT: C 427 ASN cc_start: 0.8226 (p0) cc_final: 0.7972 (p0) REVERT: D 42 MET cc_start: 0.7575 (mtp) cc_final: 0.7355 (mtp) REVERT: D 50 ASP cc_start: 0.8503 (m-30) cc_final: 0.7910 (p0) REVERT: D 118 ASN cc_start: 0.9527 (m-40) cc_final: 0.9211 (m-40) REVERT: D 160 LEU cc_start: 0.9236 (tp) cc_final: 0.8929 (tt) REVERT: D 301 MET cc_start: 0.8925 (mtm) cc_final: 0.8580 (mtt) REVERT: E 42 MET cc_start: 0.8322 (mtm) cc_final: 0.8091 (ptp) REVERT: E 92 GLU cc_start: 0.8873 (tt0) cc_final: 0.8448 (tm-30) REVERT: E 135 MET cc_start: 0.9200 (ttm) cc_final: 0.8982 (tmm) REVERT: E 235 MET cc_start: 0.8878 (mmt) cc_final: 0.8179 (mmm) REVERT: E 301 MET cc_start: 0.9051 (mtm) cc_final: 0.8753 (mtp) REVERT: E 348 MET cc_start: 0.8532 (mmp) cc_final: 0.8038 (mmp) REVERT: E 363 GLU cc_start: 0.9153 (tp30) cc_final: 0.8837 (tp30) REVERT: E 399 ASN cc_start: 0.8957 (p0) cc_final: 0.8514 (t0) REVERT: F 98 ASP cc_start: 0.7756 (t0) cc_final: 0.7514 (p0) REVERT: F 235 MET cc_start: 0.7410 (mtt) cc_final: 0.6516 (mtp) REVERT: F 270 MET cc_start: 0.8680 (ttt) cc_final: 0.8363 (ttt) REVERT: F 391 GLN cc_start: 0.9424 (mt0) cc_final: 0.9137 (mt0) REVERT: G 537 ASP cc_start: 0.8767 (t0) cc_final: 0.8422 (t0) REVERT: G 568 CYS cc_start: 0.8104 (m) cc_final: 0.7745 (t) REVERT: H 541 HIS cc_start: 0.8990 (m90) cc_final: 0.8754 (m170) REVERT: H 550 ARG cc_start: 0.9013 (mmp80) cc_final: 0.8731 (mmm160) REVERT: I 489 VAL cc_start: 0.3892 (t) cc_final: 0.3637 (t) REVERT: I 530 ILE cc_start: 0.8892 (tt) cc_final: 0.8665 (pt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1758 time to fit residues: 104.5466 Evaluate side-chains 291 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 92 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 235 optimal weight: 0.5980 chunk 268 optimal weight: 0.0020 chunk 5 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 302 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 296 optimal weight: 8.9990 overall best weight: 1.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 441 GLN C 195 GLN C 243 ASN F 45 ASN F 252 GLN ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.076246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.059659 restraints weight = 169326.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.061038 restraints weight = 122358.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.062017 restraints weight = 95334.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.062771 restraints weight = 78525.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.063290 restraints weight = 67627.799| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24908 Z= 0.122 Angle : 1.012 30.394 33783 Z= 0.402 Chirality : 0.041 0.177 3852 Planarity : 0.004 0.055 4422 Dihedral : 6.854 128.682 3554 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.08 % Allowed : 1.40 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.54 (0.15), residues: 3066 helix: 1.77 (0.12), residues: 1807 sheet: -0.39 (0.28), residues: 308 loop : 0.19 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 324 TYR 0.022 0.001 TYR D 122 PHE 0.013 0.001 PHE F 240 TRP 0.026 0.001 TRP A 48 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (24900) covalent geometry : angle 1.01186 / 0.40 (33777) SS BOND : bond 0.01027 / 0.52 ( 3) SS BOND : angle 1.65173 / 0.83 ( 6) hydrogen bonds : bond 0.03171 / 2.18 ( 1466) hydrogen bonds : angle 4.28843 / 3.13 ( 4128) Misc. bond : bond 0.00095 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 388 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9188 (m-30) cc_final: 0.8660 (p0) REVERT: A 194 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8953 (tp30) REVERT: A 269 MET cc_start: 0.7036 (tpt) cc_final: 0.6540 (tpt) REVERT: A 291 ASP cc_start: 0.8784 (m-30) cc_final: 0.8163 (p0) REVERT: A 345 LEU cc_start: 0.8028 (mt) cc_final: 0.7710 (mt) REVERT: A 416 MET cc_start: 0.8697 (mmt) cc_final: 0.8189 (mmm) REVERT: A 438 ILE cc_start: 0.8257 (mp) cc_final: 0.7635 (mp) REVERT: B 72 MET cc_start: 0.8815 (mtt) cc_final: 0.8547 (mtt) REVERT: B 187 ASP cc_start: 0.9061 (m-30) cc_final: 0.8858 (m-30) REVERT: B 235 MET cc_start: 0.8549 (mmp) cc_final: 0.8141 (mmm) REVERT: B 240 PHE cc_start: 0.9134 (t80) cc_final: 0.8874 (t80) REVERT: B 269 MET cc_start: 0.8994 (tpp) cc_final: 0.8624 (tpp) REVERT: B 291 ASP cc_start: 0.8859 (m-30) cc_final: 0.8601 (p0) REVERT: B 301 MET cc_start: 0.9108 (tmm) cc_final: 0.8623 (ppp) REVERT: B 348 MET cc_start: 0.7529 (mtp) cc_final: 0.7166 (ttm) REVERT: B 364 ILE cc_start: 0.8693 (mt) cc_final: 0.8468 (mt) REVERT: B 414 LEU cc_start: 0.9168 (tp) cc_final: 0.8681 (tt) REVERT: C 235 MET cc_start: 0.8972 (mmp) cc_final: 0.8652 (mmm) REVERT: C 250 MET cc_start: 0.8674 (tmm) cc_final: 0.8457 (tmm) REVERT: C 312 ILE cc_start: 0.9382 (mp) cc_final: 0.8968 (tt) REVERT: C 322 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 382 LEU cc_start: 0.8865 (mt) cc_final: 0.8475 (mt) REVERT: C 419 TYR cc_start: 0.7615 (t80) cc_final: 0.7090 (t80) REVERT: C 427 ASN cc_start: 0.8212 (p0) cc_final: 0.7982 (p0) REVERT: D 42 MET cc_start: 0.7537 (mtp) cc_final: 0.7249 (mtp) REVERT: D 50 ASP cc_start: 0.8493 (m-30) cc_final: 0.7893 (p0) REVERT: D 118 ASN cc_start: 0.9440 (m-40) cc_final: 0.9069 (m-40) REVERT: D 160 LEU cc_start: 0.9282 (tp) cc_final: 0.8985 (tt) REVERT: D 235 MET cc_start: 0.8889 (mmp) cc_final: 0.8666 (mmp) REVERT: D 301 MET cc_start: 0.8872 (mtm) cc_final: 0.8527 (mtt) REVERT: E 42 MET cc_start: 0.8218 (mtm) cc_final: 0.8009 (ptp) REVERT: E 92 GLU cc_start: 0.8822 (tt0) cc_final: 0.8372 (tm-30) REVERT: E 187 ASP cc_start: 0.8499 (m-30) cc_final: 0.8234 (p0) REVERT: E 235 MET cc_start: 0.8699 (mmt) cc_final: 0.8016 (mmm) REVERT: E 263 MET cc_start: 0.8470 (mtp) cc_final: 0.8036 (mpp) REVERT: E 301 MET cc_start: 0.8915 (mtm) cc_final: 0.8652 (mtp) REVERT: E 348 MET cc_start: 0.8479 (mmp) cc_final: 0.8021 (mmp) REVERT: E 363 GLU cc_start: 0.9143 (tp30) cc_final: 0.8919 (tp30) REVERT: E 373 LYS cc_start: 0.9558 (mmmt) cc_final: 0.9350 (mmmm) REVERT: F 98 ASP cc_start: 0.7897 (t0) cc_final: 0.7654 (p0) REVERT: F 235 MET cc_start: 0.7386 (mtt) cc_final: 0.6561 (mtp) REVERT: F 263 MET cc_start: 0.6911 (mpp) cc_final: 0.6692 (mpp) REVERT: F 270 MET cc_start: 0.8555 (ttt) cc_final: 0.8160 (ttt) REVERT: F 391 GLN cc_start: 0.9427 (mt0) cc_final: 0.9121 (mt0) REVERT: G 537 ASP cc_start: 0.8727 (t0) cc_final: 0.8386 (t0) REVERT: G 568 CYS cc_start: 0.8055 (m) cc_final: 0.7647 (t) REVERT: H 539 LEU cc_start: 0.9234 (mm) cc_final: 0.9020 (pp) REVERT: H 541 HIS cc_start: 0.9005 (m90) cc_final: 0.8801 (m-70) REVERT: H 550 ARG cc_start: 0.9035 (mmp80) cc_final: 0.8745 (mmm160) REVERT: I 489 VAL cc_start: 0.3954 (t) cc_final: 0.3718 (t) REVERT: I 530 ILE cc_start: 0.8861 (tt) cc_final: 0.8631 (pt) outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.1737 time to fit residues: 106.6607 Evaluate side-chains 291 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 52 optimal weight: 20.0000 chunk 270 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 139 optimal weight: 0.0770 chunk 206 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 441 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.075512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.058979 restraints weight = 169697.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.060323 restraints weight = 122066.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.061294 restraints weight = 94901.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.062004 restraints weight = 78219.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.062552 restraints weight = 67330.533| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24908 Z= 0.132 Angle : 1.015 30.520 33783 Z= 0.406 Chirality : 0.041 0.196 3852 Planarity : 0.004 0.049 4422 Dihedral : 6.780 128.752 3554 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.52 (0.15), residues: 3066 helix: 1.76 (0.12), residues: 1807 sheet: -0.38 (0.28), residues: 306 loop : 0.15 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 349 TYR 0.024 0.001 TYR D 122 PHE 0.013 0.001 PHE C 69 TRP 0.037 0.002 TRP E 48 HIS 0.007 0.001 HIS G 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (24900) covalent geometry : angle 1.01535 / 0.41 (33777) SS BOND : bond 0.00831 / 0.43 ( 3) SS BOND : angle 1.50320 / 0.73 ( 6) hydrogen bonds : bond 0.03061 / 2.11 ( 1466) hydrogen bonds : angle 4.32991 / 3.14 ( 4128) Misc. bond : bond 0.00112 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9215 (m-30) cc_final: 0.8690 (p0) REVERT: A 160 LEU cc_start: 0.9253 (tp) cc_final: 0.9037 (tp) REVERT: A 167 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8593 (mttt) REVERT: A 194 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8975 (tp30) REVERT: A 269 MET cc_start: 0.6939 (tpt) cc_final: 0.6429 (tpt) REVERT: A 291 ASP cc_start: 0.8821 (m-30) cc_final: 0.8207 (p0) REVERT: A 416 MET cc_start: 0.8729 (mmt) cc_final: 0.8152 (mmm) REVERT: A 438 ILE cc_start: 0.8179 (mp) cc_final: 0.7538 (mp) REVERT: A 451 LEU cc_start: 0.8924 (mt) cc_final: 0.8679 (mt) REVERT: B 72 MET cc_start: 0.8873 (mtt) cc_final: 0.8620 (mtt) REVERT: B 187 ASP cc_start: 0.9046 (m-30) cc_final: 0.8822 (m-30) REVERT: B 235 MET cc_start: 0.8523 (mmp) cc_final: 0.8103 (mmm) REVERT: B 240 PHE cc_start: 0.9147 (t80) cc_final: 0.8826 (t80) REVERT: B 269 MET cc_start: 0.8983 (tpp) cc_final: 0.8600 (tpp) REVERT: B 291 ASP cc_start: 0.8951 (m-30) cc_final: 0.8659 (p0) REVERT: B 301 MET cc_start: 0.9136 (tmm) cc_final: 0.8670 (ppp) REVERT: B 348 MET cc_start: 0.7633 (mtp) cc_final: 0.7228 (ttm) REVERT: B 364 ILE cc_start: 0.8711 (mt) cc_final: 0.8466 (mt) REVERT: C 235 MET cc_start: 0.8945 (mmp) cc_final: 0.8646 (mmm) REVERT: C 250 MET cc_start: 0.8745 (tmm) cc_final: 0.8514 (tmm) REVERT: C 312 ILE cc_start: 0.9432 (mp) cc_final: 0.8984 (tt) REVERT: C 322 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 337 ILE cc_start: 0.8919 (tt) cc_final: 0.8358 (mt) REVERT: C 339 LEU cc_start: 0.9457 (tt) cc_final: 0.9240 (tt) REVERT: C 382 LEU cc_start: 0.8908 (mt) cc_final: 0.8692 (mt) REVERT: C 419 TYR cc_start: 0.7651 (t80) cc_final: 0.7137 (t80) REVERT: C 427 ASN cc_start: 0.8266 (p0) cc_final: 0.8035 (p0) REVERT: D 118 ASN cc_start: 0.9477 (m-40) cc_final: 0.9102 (m-40) REVERT: D 135 MET cc_start: 0.8951 (ppp) cc_final: 0.8488 (ppp) REVERT: D 160 LEU cc_start: 0.9304 (tp) cc_final: 0.9028 (tt) REVERT: D 270 MET cc_start: 0.8992 (ttm) cc_final: 0.8367 (tmm) REVERT: D 301 MET cc_start: 0.8925 (mtm) cc_final: 0.8556 (mtt) REVERT: E 92 GLU cc_start: 0.8875 (tt0) cc_final: 0.8446 (tm-30) REVERT: E 187 ASP cc_start: 0.8577 (m-30) cc_final: 0.8319 (p0) REVERT: E 235 MET cc_start: 0.8713 (mmt) cc_final: 0.8066 (mmm) REVERT: E 263 MET cc_start: 0.8439 (mtp) cc_final: 0.7934 (mpp) REVERT: E 301 MET cc_start: 0.8911 (mtm) cc_final: 0.8710 (mtp) REVERT: E 348 MET cc_start: 0.8538 (mmp) cc_final: 0.8031 (mmp) REVERT: E 373 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9358 (mmmm) REVERT: E 426 GLU cc_start: 0.8524 (pm20) cc_final: 0.8312 (pm20) REVERT: F 98 ASP cc_start: 0.7894 (t0) cc_final: 0.7655 (p0) REVERT: F 235 MET cc_start: 0.7386 (mtt) cc_final: 0.6542 (mtp) REVERT: F 263 MET cc_start: 0.7032 (mpp) cc_final: 0.6764 (mpp) REVERT: F 270 MET cc_start: 0.8566 (ttt) cc_final: 0.8289 (ttt) REVERT: F 391 GLN cc_start: 0.9428 (mt0) cc_final: 0.9103 (mt0) REVERT: G 468 VAL cc_start: 0.6413 (t) cc_final: 0.6213 (t) REVERT: G 512 ASN cc_start: 0.8025 (t0) cc_final: 0.6922 (m110) REVERT: G 537 ASP cc_start: 0.8717 (t0) cc_final: 0.8384 (t0) REVERT: G 568 CYS cc_start: 0.8057 (m) cc_final: 0.7573 (t) REVERT: H 539 LEU cc_start: 0.9248 (mm) cc_final: 0.9029 (pp) REVERT: H 541 HIS cc_start: 0.9022 (m90) cc_final: 0.8793 (m-70) REVERT: H 550 ARG cc_start: 0.9035 (mmp80) cc_final: 0.8744 (mmm160) REVERT: I 489 VAL cc_start: 0.3967 (t) cc_final: 0.3593 (t) REVERT: I 530 ILE cc_start: 0.8861 (tt) cc_final: 0.8630 (pt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1679 time to fit residues: 97.3399 Evaluate side-chains 287 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 33 optimal weight: 0.3980 chunk 258 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 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 = 0.4033 r_free = 0.4033 target = 0.074537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.058150 restraints weight = 171328.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.059468 restraints weight = 123836.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.060426 restraints weight = 96135.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.061146 restraints weight = 79112.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.061633 restraints weight = 68100.574| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24908 Z= 0.153 Angle : 1.028 30.488 33783 Z= 0.414 Chirality : 0.041 0.253 3852 Planarity : 0.004 0.049 4422 Dihedral : 6.822 129.437 3554 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.42 (0.15), residues: 3066 helix: 1.68 (0.12), residues: 1807 sheet: -0.50 (0.28), residues: 312 loop : 0.16 (0.22), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 387 TYR 0.029 0.002 TYR D 122 PHE 0.017 0.001 PHE C 69 TRP 0.023 0.002 TRP A 48 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (24900) covalent geometry : angle 1.02738 / 0.41 (33777) SS BOND : bond 0.00875 / 0.45 ( 3) SS BOND : angle 1.83871 / 0.95 ( 6) hydrogen bonds : bond 0.03126 / 2.16 ( 1466) hydrogen bonds : angle 4.38036 / 3.18 ( 4128) Misc. bond : bond 0.00125 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9208 (m-30) cc_final: 0.8674 (p0) REVERT: A 135 MET cc_start: 0.9181 (mmt) cc_final: 0.8927 (mmm) REVERT: A 160 LEU cc_start: 0.9268 (tp) cc_final: 0.9019 (tp) REVERT: A 167 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8554 (mttt) REVERT: A 269 MET cc_start: 0.7034 (tpt) cc_final: 0.6505 (tpt) REVERT: A 291 ASP cc_start: 0.8864 (m-30) cc_final: 0.8244 (p0) REVERT: A 416 MET cc_start: 0.8654 (mmt) cc_final: 0.8217 (mmm) REVERT: A 440 LYS cc_start: 0.8842 (pttp) cc_final: 0.8527 (pttm) REVERT: A 451 LEU cc_start: 0.8936 (mt) cc_final: 0.8677 (mt) REVERT: B 72 MET cc_start: 0.8853 (mtt) cc_final: 0.8554 (mtt) REVERT: B 82 ILE cc_start: 0.8196 (mt) cc_final: 0.7936 (mt) REVERT: B 187 ASP cc_start: 0.9030 (m-30) cc_final: 0.8795 (m-30) REVERT: B 235 MET cc_start: 0.8664 (mmp) cc_final: 0.8272 (mmm) REVERT: B 240 PHE cc_start: 0.9112 (t80) cc_final: 0.8787 (t80) REVERT: B 269 MET cc_start: 0.8964 (tpp) cc_final: 0.8597 (tpp) REVERT: B 291 ASP cc_start: 0.8894 (m-30) cc_final: 0.8660 (p0) REVERT: B 297 ILE cc_start: 0.9424 (mm) cc_final: 0.9192 (pt) REVERT: B 301 MET cc_start: 0.9122 (tmm) cc_final: 0.8799 (tmm) REVERT: B 348 MET cc_start: 0.7639 (mtp) cc_final: 0.7214 (ttm) REVERT: B 364 ILE cc_start: 0.8773 (mt) cc_final: 0.8534 (mt) REVERT: C 235 MET cc_start: 0.8925 (mmp) cc_final: 0.8636 (mmm) REVERT: C 250 MET cc_start: 0.8729 (tmm) cc_final: 0.8500 (tmm) REVERT: C 312 ILE cc_start: 0.9411 (mp) cc_final: 0.8982 (tt) REVERT: C 322 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8008 (mt-10) REVERT: C 382 LEU cc_start: 0.8965 (mt) cc_final: 0.8758 (mt) REVERT: C 419 TYR cc_start: 0.7566 (t80) cc_final: 0.7103 (t80) REVERT: C 427 ASN cc_start: 0.8326 (p0) cc_final: 0.8096 (p0) REVERT: D 118 ASN cc_start: 0.9539 (m-40) cc_final: 0.9182 (m-40) REVERT: D 135 MET cc_start: 0.8970 (ppp) cc_final: 0.8644 (ppp) REVERT: D 160 LEU cc_start: 0.9261 (tp) cc_final: 0.8991 (tt) REVERT: D 270 MET cc_start: 0.8968 (ttm) cc_final: 0.8409 (tmm) REVERT: D 301 MET cc_start: 0.8891 (mtm) cc_final: 0.8530 (mtt) REVERT: D 348 MET cc_start: 0.8548 (tpp) cc_final: 0.8060 (tpp) REVERT: E 42 MET cc_start: 0.8589 (ptp) cc_final: 0.7804 (ppp) REVERT: E 92 GLU cc_start: 0.8868 (tt0) cc_final: 0.8440 (tm-30) REVERT: E 235 MET cc_start: 0.8748 (mmt) cc_final: 0.8094 (mmm) REVERT: E 263 MET cc_start: 0.8357 (mtp) cc_final: 0.7908 (mpp) REVERT: E 348 MET cc_start: 0.8599 (mmp) cc_final: 0.8078 (mmp) REVERT: F 98 ASP cc_start: 0.7910 (t0) cc_final: 0.7652 (p0) REVERT: F 301 MET cc_start: 0.8825 (mtm) cc_final: 0.8472 (tpt) REVERT: F 391 GLN cc_start: 0.9428 (mt0) cc_final: 0.9133 (mt0) REVERT: G 512 ASN cc_start: 0.8040 (t0) cc_final: 0.6918 (m110) REVERT: G 537 ASP cc_start: 0.8763 (t0) cc_final: 0.8431 (t0) REVERT: G 568 CYS cc_start: 0.8059 (m) cc_final: 0.7734 (p) REVERT: H 539 LEU cc_start: 0.9252 (mm) cc_final: 0.9034 (pp) REVERT: H 541 HIS cc_start: 0.9037 (m90) cc_final: 0.8796 (m-70) REVERT: H 550 ARG cc_start: 0.9039 (mmp80) cc_final: 0.8743 (mmm160) REVERT: I 489 VAL cc_start: 0.3830 (t) cc_final: 0.3546 (t) REVERT: I 530 ILE cc_start: 0.8854 (tt) cc_final: 0.8625 (pt) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1597 time to fit residues: 90.3541 Evaluate side-chains 283 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 60 optimal weight: 9.9990 chunk 295 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 9 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 171 optimal weight: 0.0970 chunk 142 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.075124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.058394 restraints weight = 171765.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.059835 restraints weight = 121035.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.060852 restraints weight = 92644.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.061611 restraints weight = 75829.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.062172 restraints weight = 64812.191| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24908 Z= 0.137 Angle : 1.029 30.334 33783 Z= 0.415 Chirality : 0.042 0.256 3852 Planarity : 0.004 0.049 4422 Dihedral : 6.794 129.051 3554 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.42 (0.15), residues: 3066 helix: 1.72 (0.12), residues: 1797 sheet: -0.53 (0.28), residues: 304 loop : 0.11 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 285 TYR 0.026 0.001 TYR D 122 PHE 0.026 0.002 PHE C 147 TRP 0.033 0.002 TRP D 457 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (24900) covalent geometry : angle 1.02870 / 0.41 (33777) SS BOND : bond 0.01045 / 0.53 ( 3) SS BOND : angle 2.64028 / 1.28 ( 6) hydrogen bonds : bond 0.03110 / 2.14 ( 1466) hydrogen bonds : angle 4.38212 / 3.18 ( 4128) Misc. bond : bond 0.00116 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9208 (m-30) cc_final: 0.8669 (p0) REVERT: A 135 MET cc_start: 0.9231 (mmt) cc_final: 0.8987 (mmm) REVERT: A 240 PHE cc_start: 0.9286 (t80) cc_final: 0.9085 (t80) REVERT: A 269 MET cc_start: 0.6876 (tpt) cc_final: 0.6367 (tpt) REVERT: A 291 ASP cc_start: 0.8861 (m-30) cc_final: 0.8261 (p0) REVERT: A 416 MET cc_start: 0.8804 (mmt) cc_final: 0.8497 (mmp) REVERT: A 451 LEU cc_start: 0.8945 (mt) cc_final: 0.8694 (mt) REVERT: B 42 MET cc_start: 0.8251 (mtp) cc_final: 0.8042 (mtp) REVERT: B 72 MET cc_start: 0.8858 (mtt) cc_final: 0.8554 (mtt) REVERT: B 82 ILE cc_start: 0.8197 (mt) cc_final: 0.7922 (mt) REVERT: B 187 ASP cc_start: 0.9043 (m-30) cc_final: 0.8807 (m-30) REVERT: B 225 ASP cc_start: 0.7535 (m-30) cc_final: 0.7301 (m-30) REVERT: B 235 MET cc_start: 0.8495 (mmp) cc_final: 0.8116 (mmm) REVERT: B 240 PHE cc_start: 0.9142 (t80) cc_final: 0.8813 (t80) REVERT: B 269 MET cc_start: 0.8940 (tpp) cc_final: 0.8550 (tpp) REVERT: B 291 ASP cc_start: 0.8905 (m-30) cc_final: 0.8635 (p0) REVERT: B 301 MET cc_start: 0.9139 (tmm) cc_final: 0.8671 (ppp) REVERT: B 348 MET cc_start: 0.7589 (mtp) cc_final: 0.7218 (ttm) REVERT: B 364 ILE cc_start: 0.8774 (mt) cc_final: 0.8521 (mt) REVERT: C 235 MET cc_start: 0.8886 (mmp) cc_final: 0.8613 (mmm) REVERT: C 250 MET cc_start: 0.8764 (tmm) cc_final: 0.8529 (tmm) REVERT: C 312 ILE cc_start: 0.9383 (mp) cc_final: 0.8932 (tt) REVERT: C 322 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8118 (mt-10) REVERT: C 382 LEU cc_start: 0.8971 (mt) cc_final: 0.8766 (mt) REVERT: C 419 TYR cc_start: 0.7482 (t80) cc_final: 0.7117 (t80) REVERT: C 427 ASN cc_start: 0.8337 (p0) cc_final: 0.8112 (p0) REVERT: D 118 ASN cc_start: 0.9514 (m-40) cc_final: 0.9233 (m-40) REVERT: D 135 MET cc_start: 0.8947 (ppp) cc_final: 0.8614 (ppp) REVERT: D 160 LEU cc_start: 0.9263 (tp) cc_final: 0.8994 (tt) REVERT: D 301 MET cc_start: 0.8901 (mtm) cc_final: 0.8537 (mtt) REVERT: D 348 MET cc_start: 0.8599 (tpp) cc_final: 0.8314 (tpp) REVERT: E 92 GLU cc_start: 0.8818 (tt0) cc_final: 0.8429 (tm-30) REVERT: E 235 MET cc_start: 0.8691 (mmt) cc_final: 0.8047 (mmm) REVERT: E 263 MET cc_start: 0.8364 (mtp) cc_final: 0.7914 (mpp) REVERT: E 344 TYR cc_start: 0.8076 (p90) cc_final: 0.7816 (p90) REVERT: E 348 MET cc_start: 0.8654 (mmp) cc_final: 0.8111 (mmp) REVERT: E 373 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9364 (mmmm) REVERT: F 98 ASP cc_start: 0.7874 (t0) cc_final: 0.7631 (p0) REVERT: F 235 MET cc_start: 0.7306 (mtt) cc_final: 0.6399 (mtp) REVERT: F 391 GLN cc_start: 0.9409 (mt0) cc_final: 0.9079 (mt0) REVERT: G 537 ASP cc_start: 0.8781 (t0) cc_final: 0.8461 (t0) REVERT: G 568 CYS cc_start: 0.7976 (m) cc_final: 0.7690 (p) REVERT: H 539 LEU cc_start: 0.9254 (mm) cc_final: 0.9038 (pp) REVERT: H 541 HIS cc_start: 0.9058 (m90) cc_final: 0.8840 (m-70) REVERT: H 550 ARG cc_start: 0.9047 (mmp80) cc_final: 0.8741 (mmm160) REVERT: I 489 VAL cc_start: 0.3705 (t) cc_final: 0.3490 (t) REVERT: I 530 ILE cc_start: 0.8849 (tt) cc_final: 0.8609 (pt) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1715 time to fit residues: 95.3408 Evaluate side-chains 272 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 299 optimal weight: 30.0000 chunk 77 optimal weight: 0.0670 chunk 164 optimal weight: 3.9990 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS G 551 GLN ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.072804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.056449 restraints weight = 175691.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.057809 restraints weight = 124252.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.058788 restraints weight = 95553.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.059492 restraints weight = 78353.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.060013 restraints weight = 67373.325| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24908 Z= 0.201 Angle : 1.067 31.474 33783 Z= 0.439 Chirality : 0.043 0.241 3852 Planarity : 0.004 0.064 4422 Dihedral : 7.051 132.353 3554 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.19 (0.15), residues: 3066 helix: 1.53 (0.12), residues: 1796 sheet: -0.72 (0.28), residues: 307 loop : 0.05 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 328 TYR 0.027 0.002 TYR D 122 PHE 0.036 0.002 PHE C 166 TRP 0.033 0.002 TRP D 457 HIS 0.006 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (24900) covalent geometry : angle 1.06695 / 0.44 (33777) SS BOND : bond 0.01052 / 0.54 ( 3) SS BOND : angle 2.53971 / 1.31 ( 6) hydrogen bonds : bond 0.03326 / 2.29 ( 1466) hydrogen bonds : angle 4.55182 / 3.32 ( 4128) Misc. bond : bond 0.00171 / 0.09 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9172 (m-30) cc_final: 0.8632 (p0) REVERT: A 84 LEU cc_start: 0.9327 (pp) cc_final: 0.9007 (mt) REVERT: A 135 MET cc_start: 0.9269 (mmt) cc_final: 0.9008 (mmm) REVERT: A 160 LEU cc_start: 0.9259 (tp) cc_final: 0.9019 (tp) REVERT: A 167 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8580 (mttt) REVERT: A 291 ASP cc_start: 0.8896 (m-30) cc_final: 0.8270 (p0) REVERT: A 416 MET cc_start: 0.8855 (mmt) cc_final: 0.8556 (mmp) REVERT: A 451 LEU cc_start: 0.8987 (mt) cc_final: 0.8747 (mt) REVERT: B 42 MET cc_start: 0.8274 (mtp) cc_final: 0.8003 (mtp) REVERT: B 72 MET cc_start: 0.8824 (mtt) cc_final: 0.8527 (mtt) REVERT: B 82 ILE cc_start: 0.8362 (mt) cc_final: 0.8124 (mt) REVERT: B 187 ASP cc_start: 0.8981 (m-30) cc_final: 0.8757 (m-30) REVERT: B 225 ASP cc_start: 0.7594 (m-30) cc_final: 0.7353 (m-30) REVERT: B 235 MET cc_start: 0.8639 (mmp) cc_final: 0.7999 (mmm) REVERT: B 240 PHE cc_start: 0.9102 (t80) cc_final: 0.8795 (t80) REVERT: B 269 MET cc_start: 0.8924 (tpp) cc_final: 0.8513 (tpp) REVERT: B 291 ASP cc_start: 0.8930 (m-30) cc_final: 0.8657 (p0) REVERT: B 301 MET cc_start: 0.9152 (tmm) cc_final: 0.8803 (tmm) REVERT: B 411 ASP cc_start: 0.8034 (m-30) cc_final: 0.7276 (t0) REVERT: C 160 LEU cc_start: 0.9548 (tt) cc_final: 0.8889 (pp) REVERT: C 235 MET cc_start: 0.8877 (mmp) cc_final: 0.8627 (mmm) REVERT: C 250 MET cc_start: 0.8807 (tmm) cc_final: 0.8569 (tmm) REVERT: C 312 ILE cc_start: 0.9412 (mp) cc_final: 0.8978 (tt) REVERT: C 322 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 382 LEU cc_start: 0.9058 (mt) cc_final: 0.8833 (mt) REVERT: C 419 TYR cc_start: 0.7444 (t80) cc_final: 0.6889 (t80) REVERT: D 50 ASP cc_start: 0.8537 (m-30) cc_final: 0.7860 (p0) REVERT: D 118 ASN cc_start: 0.9542 (m-40) cc_final: 0.9225 (m-40) REVERT: D 160 LEU cc_start: 0.9256 (tp) cc_final: 0.9008 (tt) REVERT: D 270 MET cc_start: 0.9198 (ttt) cc_final: 0.8080 (tmm) REVERT: D 281 GLN cc_start: 0.7776 (tt0) cc_final: 0.7083 (tm-30) REVERT: D 301 MET cc_start: 0.8938 (mtm) cc_final: 0.8602 (mtp) REVERT: D 348 MET cc_start: 0.8580 (tpp) cc_final: 0.8205 (tpp) REVERT: E 72 MET cc_start: 0.8120 (mtt) cc_final: 0.7828 (mtm) REVERT: E 92 GLU cc_start: 0.8811 (tt0) cc_final: 0.8409 (tm-30) REVERT: E 235 MET cc_start: 0.8751 (mmt) cc_final: 0.8144 (mmm) REVERT: E 348 MET cc_start: 0.8707 (mmp) cc_final: 0.8213 (mmp) REVERT: E 363 GLU cc_start: 0.9167 (tp30) cc_final: 0.8940 (tp30) REVERT: F 98 ASP cc_start: 0.7826 (t0) cc_final: 0.7577 (p0) REVERT: F 192 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7748 (tpp-160) REVERT: F 235 MET cc_start: 0.7379 (mtt) cc_final: 0.6627 (mtp) REVERT: F 270 MET cc_start: 0.8610 (ttt) cc_final: 0.8296 (ttt) REVERT: F 301 MET cc_start: 0.8808 (mtm) cc_final: 0.8462 (mmm) REVERT: F 391 GLN cc_start: 0.9386 (mt0) cc_final: 0.9008 (mt0) REVERT: G 537 ASP cc_start: 0.8767 (t0) cc_final: 0.8443 (t0) REVERT: G 568 CYS cc_start: 0.8112 (m) cc_final: 0.7799 (p) REVERT: H 541 HIS cc_start: 0.9034 (m90) cc_final: 0.8778 (m-70) REVERT: H 550 ARG cc_start: 0.9039 (mmp80) cc_final: 0.8735 (mmm160) REVERT: I 489 VAL cc_start: 0.3625 (t) cc_final: 0.3415 (t) REVERT: I 530 ILE cc_start: 0.8826 (tt) cc_final: 0.8590 (pt) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1703 time to fit residues: 91.7613 Evaluate side-chains 268 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 176 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 284 optimal weight: 0.4980 chunk 272 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN B 243 ASN B 252 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.075786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.059084 restraints weight = 170573.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.060532 restraints weight = 120314.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.061577 restraints weight = 92239.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.062270 restraints weight = 75223.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.062878 restraints weight = 64712.877| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24908 Z= 0.125 Angle : 1.053 31.567 33783 Z= 0.422 Chirality : 0.043 0.364 3852 Planarity : 0.004 0.063 4422 Dihedral : 6.863 128.295 3554 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.36 (0.15), residues: 3066 helix: 1.64 (0.12), residues: 1796 sheet: -0.56 (0.29), residues: 298 loop : 0.16 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 164 TYR 0.032 0.002 TYR F 105 PHE 0.017 0.001 PHE E 60 TRP 0.023 0.002 TRP D 457 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (24900) covalent geometry : angle 1.05219 / 0.42 (33777) SS BOND : bond 0.01088 / 0.55 ( 3) SS BOND : angle 2.39131 / 1.14 ( 6) hydrogen bonds : bond 0.03161 / 2.19 ( 1466) hydrogen bonds : angle 4.37064 / 3.17 ( 4128) Misc. bond : bond 0.00074 / 0.04 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5244.86 seconds wall clock time: 91 minutes 7.81 seconds (5467.81 seconds total)