Starting phenix.real_space_refine on Sun Sep 13 16:54:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t22_25609/09_2026/7t22_25609.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t22_25609/09_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_25609/09_2026/7t22_25609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2026/7t22_25609.map" model { file = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2026/7t22_25609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2026/7t22_25609.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2026/7t22_25609.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_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-2.2.1-6174/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: 5.23, per 1000 atoms: 0.21 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: 2.33 Conformation dependent library (CDL) restraints added in 884.1 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: 0.74 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: 5.34 Time building geometry restraints manager: 3.02 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: 0.010 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.120 Find NCS groups from input model: 0.620 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- 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 1.41525 / 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 : 0.863 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: symmetry clash REVERT: A 53 GLU cc_start: 0.8368 (tt0) cc_final: 0.8073 (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: 0.8094 (p0) REVERT: A 345 LEU cc_start: 0.8307 (mt) cc_final: 0.7838 (mt) REVERT: B 72 MET cc_start: 0.8897 (mtt) cc_final: 0.8636 (mtt) REVERT: B 226 LEU cc_start: 0.8288 (tp) cc_final: 0.7776 (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: 0.5791 (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: 0.8736 (p0) REVERT: B 324 ARG cc_start: 0.9166 (ttm170) cc_final: 0.8900 (ttm-80) REVERT: B 348 MET cc_start: 0.7184 (mtp) cc_final: 0.6968 (ttm) REVERT: B 414 LEU cc_start: 0.9277 (tp) cc_final: 0.8940 (tp) REVERT: C 60 PHE cc_start: 0.9225 (m-80) cc_final: 0.8922 (m-10) REVERT: C 61 TYR cc_start: 0.8669 (t80) cc_final: 0.8431 (t80) REVERT: C 240 PHE cc_start: 0.8919 (t80) cc_final: 0.8479 (t80) REVERT: C 259 PHE cc_start: 0.9023 (m-80) cc_final: 0.8751 (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: 0.8237 (mtp) REVERT: C 382 LEU cc_start: 0.8828 (mt) cc_final: 0.8328 (mt) REVERT: D 50 ASP cc_start: 0.8181 (m-30) cc_final: 0.7809 (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: 0.7933 (pp) REVERT: D 118 ASN cc_start: 0.9391 (m-40) cc_final: 0.9090 (m-40) REVERT: D 160 LEU cc_start: 0.9159 (tp) cc_final: 0.8872 (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: 0.7040 (tmm) REVERT: D 363 GLU cc_start: 0.7849 (tp30) cc_final: 0.7257 (tm-30) REVERT: D 426 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7603 (tp30) REVERT: E 60 PHE cc_start: 0.8983 (m-80) cc_final: 0.8284 (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: 0.8145 (mmm) REVERT: E 270 MET cc_start: 0.8963 (mtm) cc_final: 0.8353 (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: 0.8897 (tp30) REVERT: E 443 ASN cc_start: 0.8521 (m-40) cc_final: 0.7420 (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: 0.6463 (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: 0.8742 (pm20) REVERT: G 568 CYS cc_start: 0.8504 (m) cc_final: 0.8110 (t) REVERT: H 498 LEU cc_start: 0.0378 (pt) cc_final: -0.0331 (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: 0.1889 time to fit residues: 193.0401 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 : 0.959 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.077820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060714 restraints weight = 165195.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.062122 restraints weight = 118325.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.063205 restraints weight = 91678.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.063994 restraints weight = 75085.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.064562 restraints weight = 64164.786| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2551 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= 0.183 Angle : 1.057 30.613 33783 Z= 0.433 Chirality : 0.043 0.233 3852 Planarity : 0.005 0.104 4422 Dihedral : 7.610 123.221 3554 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.30 % Allowed : 2.24 % Favored : 97.46 % 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: 1.93 (0.15), residues: 3066 helix: 2.17 (0.12), residues: 1777 sheet: -0.57 (0.27), residues: 320 loop : 0.38 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 387 TYR 0.024 0.002 TYR B 122 PHE 0.029 0.002 PHE F 240 TRP 0.019 0.002 TRP A 48 HIS 0.008 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (24900) covalent geometry : angle 1.05675 / 0.43 (33777) SS BOND : bond 0.00714 / 0.37 ( 3) SS BOND : angle 1.71212 / 0.83 ( 6) hydrogen bonds : bond 0.04204 / 2.90 ( 1466) hydrogen bonds : angle 4.41301 / 3.20 ( 4128) Misc. bond : bond 0.00528 / 0.29 ( 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: 8 poor density : 445 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: A 58 ASP cc_start: 0.9134 (m-30) cc_final: 0.8673 (p0) REVERT: A 135 MET cc_start: 0.8806 (ttm) cc_final: 0.8500 (ppp) REVERT: A 194 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8955 (tp30) REVERT: A 291 ASP cc_start: 0.8807 (m-30) cc_final: 0.8249 (p0) REVERT: A 345 LEU cc_start: 0.8051 (mt) cc_final: 0.7755 (mt) REVERT: B 72 MET cc_start: 0.8640 (mtt) cc_final: 0.8373 (mtt) REVERT: B 235 MET cc_start: 0.8826 (mmt) cc_final: 0.8528 (mmm) REVERT: B 240 PHE cc_start: 0.9181 (t80) cc_final: 0.8929 (t80) REVERT: B 269 MET cc_start: 0.8958 (tpp) cc_final: 0.8523 (tpp) REVERT: B 291 ASP cc_start: 0.8977 (m-30) cc_final: 0.8719 (p0) REVERT: B 297 ILE cc_start: 0.9477 (mm) cc_final: 0.9231 (pt) REVERT: B 301 MET cc_start: 0.8962 (tmm) cc_final: 0.8734 (tmm) REVERT: B 324 ARG cc_start: 0.9197 (ttm170) cc_final: 0.8707 (ttt180) REVERT: B 348 MET cc_start: 0.7284 (mtp) cc_final: 0.6753 (mpp) REVERT: C 235 MET cc_start: 0.9105 (mmp) cc_final: 0.8796 (mmm) REVERT: C 259 PHE cc_start: 0.9215 (m-80) cc_final: 0.8800 (m-80) REVERT: C 263 MET cc_start: 0.8347 (mtp) cc_final: 0.8094 (ttm) REVERT: C 312 ILE cc_start: 0.9441 (mp) cc_final: 0.9028 (tt) REVERT: C 382 LEU cc_start: 0.8859 (mt) cc_final: 0.8619 (mt) REVERT: C 427 ASN cc_start: 0.8105 (p0) cc_final: 0.7763 (p0) REVERT: D 34 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8747 (mt-10) REVERT: D 58 ASP cc_start: 0.9034 (m-30) cc_final: 0.8783 (p0) REVERT: D 118 ASN cc_start: 0.9474 (m-40) cc_final: 0.9152 (m-40) REVERT: D 160 LEU cc_start: 0.9205 (tp) cc_final: 0.8907 (tt) REVERT: D 237 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8393 (ptpt) REVERT: D 269 MET cc_start: 0.8550 (ttm) cc_final: 0.8164 (ttm) REVERT: D 301 MET cc_start: 0.8900 (mtm) cc_final: 0.8567 (mtt) REVERT: D 337 ILE cc_start: 0.8694 (mt) cc_final: 0.8465 (mm) REVERT: E 60 PHE cc_start: 0.9127 (m-80) cc_final: 0.8921 (m-80) REVERT: E 85 ILE cc_start: 0.9545 (pt) cc_final: 0.9303 (mp) REVERT: E 92 GLU cc_start: 0.8816 (tt0) cc_final: 0.8562 (tm-30) REVERT: E 135 MET cc_start: 0.9282 (ttm) cc_final: 0.9063 (tmm) REVERT: E 235 MET cc_start: 0.8867 (mmt) cc_final: 0.7882 (mmm) REVERT: E 267 GLN cc_start: 0.9186 (mp10) cc_final: 0.8945 (mp10) REVERT: E 363 GLU cc_start: 0.9171 (tp30) cc_final: 0.8862 (tp30) REVERT: F 98 ASP cc_start: 0.7781 (t0) cc_final: 0.7569 (p0) REVERT: F 235 MET cc_start: 0.7339 (mtt) cc_final: 0.6464 (mtp) REVERT: F 263 MET cc_start: 0.7011 (mpp) cc_final: 0.6718 (mpp) REVERT: F 282 THR cc_start: 0.9227 (m) cc_final: 0.8922 (p) REVERT: F 318 LEU cc_start: 0.8384 (mp) cc_final: 0.8106 (mp) REVERT: G 468 VAL cc_start: 0.6758 (t) cc_final: 0.6427 (t) REVERT: G 568 CYS cc_start: 0.8133 (m) cc_final: 0.7725 (t) REVERT: H 541 HIS cc_start: 0.8769 (m90) cc_final: 0.8568 (m90) REVERT: H 550 ARG cc_start: 0.8963 (mmp80) cc_final: 0.8693 (mmm160) REVERT: I 489 VAL cc_start: 0.4232 (t) cc_final: 0.3987 (t) REVERT: I 530 ILE cc_start: 0.8877 (tt) cc_final: 0.8663 (pt) outliers start: 8 outliers final: 2 residues processed: 450 average time/residue: 0.1834 time to fit residues: 127.5471 Evaluate side-chains 316 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 0.0170 chunk 89 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 410 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.076151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.059434 restraints weight = 170547.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.060823 restraints weight = 123040.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.061802 restraints weight = 95616.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.062525 restraints weight = 78788.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.063075 restraints weight = 67795.464| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24908 Z= 0.179 Angle : 1.032 30.727 33783 Z= 0.420 Chirality : 0.041 0.220 3852 Planarity : 0.005 0.085 4422 Dihedral : 7.416 126.659 3554 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.04 % Allowed : 2.35 % 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: 1.66 (0.15), residues: 3066 helix: 1.88 (0.12), residues: 1787 sheet: -0.55 (0.27), residues: 324 loop : 0.36 (0.22), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 278 TYR 0.026 0.002 TYR B 122 PHE 0.019 0.002 PHE F 240 TRP 0.028 0.002 TRP E 48 HIS 0.012 0.002 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (24900) covalent geometry : angle 1.03171 / 0.42 (33777) SS BOND : bond 0.01310 / 0.66 ( 3) SS BOND : angle 1.85378 / 0.94 ( 6) hydrogen bonds : bond 0.03708 / 2.57 ( 1466) hydrogen bonds : angle 4.37912 / 3.19 ( 4128) Misc. bond : bond 0.00178 / 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 415 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.094 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: 0.9158 (m-30) cc_final: 0.8698 (p0) REVERT: A 135 MET cc_start: 0.8803 (ttm) cc_final: 0.8567 (ppp) REVERT: A 194 GLU cc_start: 0.9232 (mt-10) cc_final: 0.9000 (tp30) REVERT: A 242 MET cc_start: 0.8917 (ppp) cc_final: 0.8670 (ppp) REVERT: A 291 ASP cc_start: 0.8795 (m-30) cc_final: 0.8225 (p0) REVERT: A 345 LEU cc_start: 0.7939 (mt) cc_final: 0.7598 (mt) REVERT: A 348 MET cc_start: 0.9147 (ttm) cc_final: 0.8604 (ttm) REVERT: A 416 MET cc_start: 0.8595 (mmt) cc_final: 0.8067 (mmm) REVERT: A 438 ILE cc_start: 0.8337 (mp) cc_final: 0.7650 (mp) REVERT: A 440 LYS cc_start: 0.8673 (pttm) cc_final: 0.8441 (pttm) REVERT: B 72 MET cc_start: 0.8672 (mtt) cc_final: 0.8445 (mtt) REVERT: B 240 PHE cc_start: 0.9137 (t80) cc_final: 0.8920 (t80) REVERT: B 269 MET cc_start: 0.9013 (tpp) cc_final: 0.8627 (tpp) REVERT: B 291 ASP cc_start: 0.8943 (m-30) cc_final: 0.8696 (p0) REVERT: B 297 ILE cc_start: 0.9446 (mm) cc_final: 0.9209 (pt) REVERT: B 301 MET cc_start: 0.9023 (tmm) cc_final: 0.8732 (tmm) REVERT: B 348 MET cc_start: 0.7495 (mtp) cc_final: 0.7141 (ttm) REVERT: B 414 LEU cc_start: 0.9161 (tp) cc_final: 0.8794 (tp) REVERT: C 235 MET cc_start: 0.9019 (mmp) cc_final: 0.8716 (mmm) REVERT: C 259 PHE cc_start: 0.9120 (m-80) cc_final: 0.8846 (m-80) REVERT: C 322 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8162 (mt-10) REVERT: C 382 LEU cc_start: 0.8839 (mt) cc_final: 0.8337 (mt) REVERT: C 419 TYR cc_start: 0.7770 (t80) cc_final: 0.7511 (t80) REVERT: C 427 ASN cc_start: 0.8169 (p0) cc_final: 0.7884 (p0) REVERT: D 58 ASP cc_start: 0.9051 (m-30) cc_final: 0.8811 (p0) REVERT: D 118 ASN cc_start: 0.9500 (m-40) cc_final: 0.9246 (m-40) REVERT: D 160 LEU cc_start: 0.9250 (tp) cc_final: 0.8952 (tt) REVERT: D 301 MET cc_start: 0.8896 (mtm) cc_final: 0.8570 (mtt) REVERT: D 337 ILE cc_start: 0.8686 (mt) cc_final: 0.8459 (mm) REVERT: E 42 MET cc_start: 0.8390 (ptp) cc_final: 0.7355 (ppp) REVERT: E 85 ILE cc_start: 0.9542 (pt) cc_final: 0.9266 (mp) REVERT: E 92 GLU cc_start: 0.8812 (tt0) cc_final: 0.8496 (tp30) REVERT: E 135 MET cc_start: 0.9287 (ttm) cc_final: 0.9003 (tmm) REVERT: E 235 MET cc_start: 0.8899 (mmt) cc_final: 0.8308 (mmm) REVERT: E 363 GLU cc_start: 0.9165 (tp30) cc_final: 0.8846 (tp30) REVERT: E 443 ASN cc_start: 0.8282 (m-40) cc_final: 0.7131 (t0) REVERT: F 98 ASP cc_start: 0.7799 (t0) cc_final: 0.7554 (p0) REVERT: F 235 MET cc_start: 0.7482 (mtt) cc_final: 0.6710 (mtp) REVERT: F 282 THR cc_start: 0.9244 (m) cc_final: 0.8963 (p) REVERT: F 391 GLN cc_start: 0.9381 (mt0) cc_final: 0.9153 (mt0) REVERT: G 537 ASP cc_start: 0.8774 (t0) cc_final: 0.8445 (t0) REVERT: G 568 CYS cc_start: 0.8050 (m) cc_final: 0.7685 (t) REVERT: H 541 HIS cc_start: 0.8915 (m90) cc_final: 0.8696 (m170) REVERT: H 550 ARG cc_start: 0.8976 (mmp80) cc_final: 0.8698 (mmm160) REVERT: I 489 VAL cc_start: 0.4194 (t) cc_final: 0.3986 (t) REVERT: I 530 ILE cc_start: 0.8938 (tt) cc_final: 0.8713 (pt) outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 0.1817 time to fit residues: 116.7440 Evaluate side-chains 308 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 0.0980 chunk 296 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 284 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN B 281 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.076821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.059917 restraints weight = 167811.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.061279 restraints weight = 121784.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.062277 restraints weight = 95391.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.063002 restraints weight = 78776.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.063570 restraints weight = 67923.167| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3484 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= 0.134 Angle : 1.008 30.214 33783 Z= 0.403 Chirality : 0.041 0.187 3852 Planarity : 0.004 0.064 4422 Dihedral : 7.183 127.337 3554 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % 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: 1.65 (0.15), residues: 3066 helix: 1.85 (0.12), residues: 1793 sheet: -0.55 (0.27), residues: 331 loop : 0.40 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 285 TYR 0.031 0.001 TYR B 122 PHE 0.018 0.002 PHE F 240 TRP 0.022 0.001 TRP A 48 HIS 0.006 0.001 HIS G 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (24900) covalent geometry : angle 1.00807 / 0.40 (33777) SS BOND : bond 0.00917 / 0.47 ( 3) SS BOND : angle 1.62325 / 0.76 ( 6) hydrogen bonds : bond 0.03393 / 2.34 ( 1466) hydrogen bonds : angle 4.28452 / 3.13 ( 4128) Misc. bond : bond 0.00103 / 0.05 ( 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 402 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.043 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: 0.9175 (m-30) cc_final: 0.8676 (p0) REVERT: A 72 MET cc_start: 0.8524 (mmp) cc_final: 0.8314 (mmp) REVERT: A 194 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8964 (tp30) REVERT: A 242 MET cc_start: 0.8927 (ppp) cc_final: 0.8644 (ppp) REVERT: A 291 ASP cc_start: 0.8810 (m-30) cc_final: 0.8231 (p0) REVERT: A 345 LEU cc_start: 0.7901 (mt) cc_final: 0.7547 (mt) REVERT: A 416 MET cc_start: 0.8681 (mmt) cc_final: 0.8180 (mmm) REVERT: A 438 ILE cc_start: 0.8238 (mp) cc_final: 0.7596 (mp) REVERT: A 440 LYS cc_start: 0.8673 (pttm) cc_final: 0.8423 (pttm) REVERT: B 72 MET cc_start: 0.8748 (mtt) cc_final: 0.8496 (mtt) REVERT: B 240 PHE cc_start: 0.9093 (t80) cc_final: 0.8799 (t80) REVERT: B 269 MET cc_start: 0.9028 (tpp) cc_final: 0.8647 (tpp) REVERT: B 291 ASP cc_start: 0.8902 (m-30) cc_final: 0.8661 (p0) REVERT: B 301 MET cc_start: 0.9032 (tmm) cc_final: 0.8561 (ppp) REVERT: B 348 MET cc_start: 0.7407 (mtp) cc_final: 0.7120 (ttm) REVERT: C 51 VAL cc_start: 0.8334 (t) cc_final: 0.8129 (p) REVERT: C 235 MET cc_start: 0.8963 (mmp) cc_final: 0.8656 (mmm) REVERT: C 259 PHE cc_start: 0.9086 (m-80) cc_final: 0.8778 (m-80) REVERT: C 270 MET cc_start: 0.8591 (mtp) cc_final: 0.8316 (ttt) REVERT: C 312 ILE cc_start: 0.9431 (mp) cc_final: 0.9206 (pt) REVERT: C 322 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8124 (mt-10) REVERT: C 382 LEU cc_start: 0.8808 (mt) cc_final: 0.8390 (mt) REVERT: C 419 TYR cc_start: 0.7810 (t80) cc_final: 0.7433 (t80) REVERT: C 427 ASN cc_start: 0.8146 (p0) cc_final: 0.7874 (p0) REVERT: D 42 MET cc_start: 0.7362 (mtp) cc_final: 0.7072 (mtp) REVERT: D 58 ASP cc_start: 0.9059 (m-30) cc_final: 0.8791 (p0) REVERT: D 118 ASN cc_start: 0.9453 (m-40) cc_final: 0.9105 (m-40) REVERT: D 160 LEU cc_start: 0.9273 (tp) cc_final: 0.8977 (tt) REVERT: D 235 MET cc_start: 0.8904 (mmp) cc_final: 0.8666 (mmp) REVERT: D 269 MET cc_start: 0.8709 (mtp) cc_final: 0.8492 (ttm) REVERT: D 301 MET cc_start: 0.8916 (mtm) cc_final: 0.8550 (mtt) REVERT: D 360 GLU cc_start: 0.8491 (tt0) cc_final: 0.8008 (tm-30) REVERT: D 399 ASN cc_start: 0.8779 (m-40) cc_final: 0.8568 (p0) REVERT: E 42 MET cc_start: 0.8391 (ptp) cc_final: 0.7476 (ppp) REVERT: E 92 GLU cc_start: 0.8819 (tt0) cc_final: 0.8504 (tp30) REVERT: E 135 MET cc_start: 0.9222 (ttm) cc_final: 0.8971 (tmm) REVERT: E 235 MET cc_start: 0.8759 (mmt) cc_final: 0.7936 (mmm) REVERT: E 301 MET cc_start: 0.9113 (mtm) cc_final: 0.8767 (mtt) REVERT: E 348 MET cc_start: 0.8404 (mmp) cc_final: 0.7986 (mmp) REVERT: E 363 GLU cc_start: 0.9160 (tp30) cc_final: 0.8855 (tp30) REVERT: E 443 ASN cc_start: 0.8198 (m-40) cc_final: 0.7102 (t0) REVERT: F 98 ASP cc_start: 0.7817 (t0) cc_final: 0.7578 (p0) REVERT: F 235 MET cc_start: 0.7396 (mtt) cc_final: 0.6507 (mtp) REVERT: F 263 MET cc_start: 0.6832 (mpp) cc_final: 0.6591 (mpp) REVERT: F 282 THR cc_start: 0.9197 (m) cc_final: 0.8920 (p) REVERT: F 391 GLN cc_start: 0.9396 (mt0) cc_final: 0.9156 (mt0) REVERT: F 414 LEU cc_start: 0.9144 (tp) cc_final: 0.8774 (tp) REVERT: G 512 ASN cc_start: 0.7852 (t0) cc_final: 0.6727 (m110) REVERT: G 537 ASP cc_start: 0.8721 (t0) cc_final: 0.8393 (t0) REVERT: G 568 CYS cc_start: 0.8090 (m) cc_final: 0.7655 (t) REVERT: H 541 HIS cc_start: 0.8932 (m90) cc_final: 0.8706 (m170) REVERT: H 550 ARG cc_start: 0.8998 (mmp80) cc_final: 0.8719 (mmm160) REVERT: I 489 VAL cc_start: 0.4172 (t) cc_final: 0.3957 (t) REVERT: I 530 ILE cc_start: 0.8889 (tt) cc_final: 0.8674 (pt) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1874 time to fit residues: 116.7347 Evaluate side-chains 299 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 6.9990 chunk 179 optimal weight: 0.0870 chunk 282 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN C 195 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.075204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058574 restraints weight = 170412.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.059909 restraints weight = 123114.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060858 restraints weight = 95863.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.061590 restraints weight = 79289.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.062106 restraints weight = 68427.224| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 24908 Z= 0.166 Angle : 1.023 31.242 33783 Z= 0.413 Chirality : 0.041 0.164 3852 Planarity : 0.004 0.057 4422 Dihedral : 7.184 129.601 3554 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.95 % 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: 1.61 (0.15), residues: 3066 helix: 1.83 (0.12), residues: 1782 sheet: -0.55 (0.27), residues: 327 loop : 0.37 (0.22), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 387 TYR 0.024 0.001 TYR D 122 PHE 0.019 0.002 PHE B 60 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 0.00360 / 0.17 (24900) covalent geometry : angle 1.02281 / 0.41 (33777) SS BOND : bond 0.00674 / 0.34 ( 3) SS BOND : angle 2.08606 / 1.08 ( 6) hydrogen bonds : bond 0.03372 / 2.31 ( 1466) hydrogen bonds : angle 4.32169 / 3.16 ( 4128) Misc. bond : bond 0.00176 / 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 381 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.974 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: 0.9167 (m-30) cc_final: 0.8643 (p0) REVERT: A 72 MET cc_start: 0.8524 (mmp) cc_final: 0.8281 (mmp) REVERT: A 194 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8937 (tp30) REVERT: A 291 ASP cc_start: 0.8784 (m-30) cc_final: 0.8177 (p0) REVERT: A 416 MET cc_start: 0.8598 (mmt) cc_final: 0.8083 (mmm) REVERT: A 438 ILE cc_start: 0.8214 (mp) cc_final: 0.7569 (mp) REVERT: B 187 ASP cc_start: 0.8998 (m-30) cc_final: 0.8780 (m-30) REVERT: B 240 PHE cc_start: 0.9007 (t80) cc_final: 0.8723 (t80) REVERT: B 269 MET cc_start: 0.8993 (tpp) cc_final: 0.8621 (tpp) REVERT: B 291 ASP cc_start: 0.8868 (m-30) cc_final: 0.8594 (p0) REVERT: B 301 MET cc_start: 0.9056 (tmm) cc_final: 0.8711 (tmm) REVERT: B 348 MET cc_start: 0.7510 (mtp) cc_final: 0.7162 (ttm) REVERT: B 411 ASP cc_start: 0.7835 (m-30) cc_final: 0.7082 (t0) REVERT: C 51 VAL cc_start: 0.8357 (t) cc_final: 0.8110 (p) REVERT: C 235 MET cc_start: 0.8986 (mmp) cc_final: 0.8697 (mmm) REVERT: C 270 MET cc_start: 0.8677 (mtp) cc_final: 0.8400 (ttt) REVERT: C 322 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8036 (mt-10) REVERT: C 382 LEU cc_start: 0.8794 (mt) cc_final: 0.8350 (mt) REVERT: C 419 TYR cc_start: 0.7693 (t80) cc_final: 0.7222 (t80) REVERT: C 427 ASN cc_start: 0.8160 (p0) cc_final: 0.7899 (p0) REVERT: D 42 MET cc_start: 0.7456 (mtp) cc_final: 0.7199 (mtp) REVERT: D 118 ASN cc_start: 0.9479 (m-40) cc_final: 0.9134 (m-40) REVERT: D 160 LEU cc_start: 0.9246 (tp) cc_final: 0.8934 (tt) REVERT: D 269 MET cc_start: 0.8643 (mtp) cc_final: 0.8441 (ttm) REVERT: D 301 MET cc_start: 0.8887 (mtm) cc_final: 0.8538 (mtt) REVERT: E 42 MET cc_start: 0.8359 (ptp) cc_final: 0.7486 (ppp) REVERT: E 92 GLU cc_start: 0.8835 (tt0) cc_final: 0.8499 (tm-30) REVERT: E 135 MET cc_start: 0.9156 (ttm) cc_final: 0.8950 (tmm) REVERT: E 187 ASP cc_start: 0.8577 (m-30) cc_final: 0.8292 (p0) REVERT: E 235 MET cc_start: 0.8798 (mmt) cc_final: 0.8533 (mmm) REVERT: E 301 MET cc_start: 0.9038 (mtm) cc_final: 0.8628 (mtp) REVERT: E 348 MET cc_start: 0.8423 (mmp) cc_final: 0.7974 (mmp) REVERT: E 363 GLU cc_start: 0.9115 (tp30) cc_final: 0.8824 (tp30) REVERT: F 98 ASP cc_start: 0.7770 (t0) cc_final: 0.7531 (p0) REVERT: F 235 MET cc_start: 0.7382 (mtt) cc_final: 0.6471 (mtp) REVERT: F 391 GLN cc_start: 0.9436 (mt0) cc_final: 0.9169 (mt0) REVERT: F 414 LEU cc_start: 0.9051 (tp) cc_final: 0.8837 (tp) REVERT: G 537 ASP cc_start: 0.8779 (t0) cc_final: 0.8434 (t0) REVERT: G 568 CYS cc_start: 0.8065 (m) cc_final: 0.7677 (t) REVERT: H 539 LEU cc_start: 0.9236 (mm) cc_final: 0.8999 (pp) REVERT: H 541 HIS cc_start: 0.8956 (m90) cc_final: 0.8745 (m-70) REVERT: H 550 ARG cc_start: 0.9018 (mmp80) cc_final: 0.8730 (mmm160) REVERT: I 489 VAL cc_start: 0.4042 (t) cc_final: 0.3818 (t) REVERT: I 530 ILE cc_start: 0.8914 (tt) cc_final: 0.8681 (pt) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.1745 time to fit residues: 103.9020 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 : 0.898 ------------------------------------------------------------------------------- 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: 3.9990 chunk 148 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 5 optimal weight: 0.0030 chunk 289 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 302 optimal weight: 20.0000 chunk 278 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN C 243 ASN C 281 GLN F 45 ASN F 252 GLN G 541 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.076378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.059772 restraints weight = 168600.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.061162 restraints weight = 121272.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.062149 restraints weight = 93698.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062861 restraints weight = 76954.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.063345 restraints weight = 66506.916| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24908 Z= 0.123 Angle : 1.009 30.790 33783 Z= 0.403 Chirality : 0.041 0.273 3852 Planarity : 0.004 0.054 4422 Dihedral : 7.046 128.966 3554 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 1.61 (0.15), residues: 3066 helix: 1.84 (0.12), residues: 1791 sheet: -0.52 (0.28), residues: 317 loop : 0.32 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 328 TYR 0.022 0.001 TYR D 122 PHE 0.039 0.002 PHE C 166 TRP 0.025 0.001 TRP A 48 HIS 0.006 0.001 HIS G 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (24900) covalent geometry : angle 1.00857 / 0.40 (33777) SS BOND : bond 0.00901 / 0.46 ( 3) SS BOND : angle 1.77809 / 0.89 ( 6) hydrogen bonds : bond 0.03209 / 2.21 ( 1466) hydrogen bonds : angle 4.27578 / 3.14 ( 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 380 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.019 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: A 58 ASP cc_start: 0.9165 (m-30) cc_final: 0.8636 (p0) REVERT: A 72 MET cc_start: 0.8535 (mmp) cc_final: 0.8241 (mmp) REVERT: A 160 LEU cc_start: 0.9263 (tp) cc_final: 0.9041 (tp) REVERT: A 167 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8596 (mttt) REVERT: A 291 ASP cc_start: 0.8793 (m-30) cc_final: 0.8190 (p0) REVERT: A 416 MET cc_start: 0.8660 (mmt) cc_final: 0.8147 (mmm) REVERT: A 438 ILE cc_start: 0.8210 (mp) cc_final: 0.7543 (mp) REVERT: B 187 ASP cc_start: 0.9024 (m-30) cc_final: 0.8809 (m-30) REVERT: B 269 MET cc_start: 0.8981 (tpp) cc_final: 0.8613 (tpp) REVERT: B 291 ASP cc_start: 0.8889 (m-30) cc_final: 0.8637 (p0) REVERT: B 301 MET cc_start: 0.9108 (tmm) cc_final: 0.8623 (ppp) REVERT: B 311 TYR cc_start: 0.8931 (m-80) cc_final: 0.8711 (m-80) REVERT: B 348 MET cc_start: 0.7450 (mtp) cc_final: 0.7212 (ttm) REVERT: C 160 LEU cc_start: 0.9572 (tt) cc_final: 0.8836 (pp) REVERT: C 235 MET cc_start: 0.8913 (mmp) cc_final: 0.8634 (mmm) REVERT: C 250 MET cc_start: 0.8683 (tmm) cc_final: 0.8477 (tmm) REVERT: C 312 ILE cc_start: 0.9374 (mp) cc_final: 0.8939 (tt) REVERT: C 322 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 382 LEU cc_start: 0.8770 (mt) cc_final: 0.8557 (mt) REVERT: C 419 TYR cc_start: 0.7669 (t80) cc_final: 0.7232 (t80) REVERT: C 427 ASN cc_start: 0.8180 (p0) cc_final: 0.7938 (p0) REVERT: D 42 MET cc_start: 0.7396 (mtp) cc_final: 0.7050 (mtp) REVERT: D 118 ASN cc_start: 0.9446 (m-40) cc_final: 0.9025 (m-40) REVERT: D 160 LEU cc_start: 0.9285 (tp) cc_final: 0.8993 (tt) REVERT: D 235 MET cc_start: 0.8937 (mmp) cc_final: 0.8688 (mmp) REVERT: D 270 MET cc_start: 0.8847 (ttm) cc_final: 0.8025 (tmm) REVERT: D 281 GLN cc_start: 0.7537 (tt0) cc_final: 0.7117 (tm-30) REVERT: D 301 MET cc_start: 0.8898 (mtm) cc_final: 0.8529 (mtt) REVERT: E 42 MET cc_start: 0.8274 (ptp) cc_final: 0.7603 (ppp) REVERT: E 92 GLU cc_start: 0.8895 (tt0) cc_final: 0.8447 (tm-30) REVERT: E 135 MET cc_start: 0.9158 (ttm) cc_final: 0.8948 (tmm) REVERT: E 167 LYS cc_start: 0.9266 (pttp) cc_final: 0.8995 (pttt) REVERT: E 187 ASP cc_start: 0.8576 (m-30) cc_final: 0.8303 (p0) REVERT: E 235 MET cc_start: 0.8653 (mmt) cc_final: 0.8432 (mmm) REVERT: E 263 MET cc_start: 0.8396 (mtp) cc_final: 0.7931 (mpp) REVERT: E 301 MET cc_start: 0.8972 (mtm) cc_final: 0.8673 (mtp) REVERT: E 344 TYR cc_start: 0.7990 (p90) cc_final: 0.7719 (p90) REVERT: E 348 MET cc_start: 0.8449 (mmp) cc_final: 0.7984 (mmp) REVERT: E 363 GLU cc_start: 0.9143 (tp30) cc_final: 0.8917 (tp30) REVERT: E 373 LYS cc_start: 0.9537 (mmmt) cc_final: 0.9327 (mmmm) REVERT: E 399 ASN cc_start: 0.8760 (p0) cc_final: 0.8490 (t0) REVERT: F 72 MET cc_start: 0.9016 (ptp) cc_final: 0.8678 (ptt) REVERT: F 98 ASP cc_start: 0.7881 (t0) cc_final: 0.7635 (p0) REVERT: F 235 MET cc_start: 0.7294 (mtt) cc_final: 0.6454 (mtp) REVERT: F 391 GLN cc_start: 0.9426 (mt0) cc_final: 0.9137 (mt0) REVERT: G 468 VAL cc_start: 0.6451 (t) cc_final: 0.6245 (t) REVERT: G 537 ASP cc_start: 0.8732 (t0) cc_final: 0.8394 (t0) REVERT: G 568 CYS cc_start: 0.8025 (m) cc_final: 0.7621 (t) REVERT: H 539 LEU cc_start: 0.9228 (mm) cc_final: 0.9018 (pp) REVERT: H 541 HIS cc_start: 0.8985 (m90) cc_final: 0.8772 (m-70) REVERT: H 550 ARG cc_start: 0.9027 (mmp80) cc_final: 0.8735 (mmm160) REVERT: I 489 VAL cc_start: 0.3956 (t) cc_final: 0.3749 (t) REVERT: I 530 ILE cc_start: 0.8868 (tt) cc_final: 0.8637 (pt) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.1679 time to fit residues: 100.6268 Evaluate side-chains 286 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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: 10.0000 chunk 270 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN 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 = 0.4020 r_free = 0.4020 target = 0.073617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.057094 restraints weight = 177198.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058478 restraints weight = 125500.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.059464 restraints weight = 96183.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.060216 restraints weight = 78639.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060743 restraints weight = 67357.310| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24908 Z= 0.192 Angle : 1.062 31.737 33783 Z= 0.433 Chirality : 0.042 0.360 3852 Planarity : 0.005 0.146 4422 Dihedral : 7.185 132.472 3554 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.48 (0.15), residues: 3066 helix: 1.71 (0.12), residues: 1781 sheet: -0.63 (0.28), residues: 318 loop : 0.37 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 349 TYR 0.027 0.002 TYR D 122 PHE 0.022 0.002 PHE B 60 TRP 0.035 0.002 TRP F 457 HIS 0.005 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (24900) covalent geometry : angle 1.06142 / 0.43 (33777) SS BOND : bond 0.00868 / 0.45 ( 3) SS BOND : angle 1.50526 / 0.76 ( 6) hydrogen bonds : bond 0.03343 / 2.30 ( 1466) hydrogen bonds : angle 4.44961 / 3.25 ( 4128) Misc. bond : bond 0.00204 / 0.11 ( 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 361 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.063 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: A 58 ASP cc_start: 0.9197 (m-30) cc_final: 0.8673 (p0) REVERT: A 72 MET cc_start: 0.8463 (mmp) cc_final: 0.8224 (mmp) REVERT: A 84 LEU cc_start: 0.9276 (pp) cc_final: 0.8984 (mt) REVERT: A 291 ASP cc_start: 0.8842 (m-30) cc_final: 0.8219 (p0) REVERT: A 416 MET cc_start: 0.8618 (mmt) cc_final: 0.8340 (mmp) REVERT: A 438 ILE cc_start: 0.8215 (mp) cc_final: 0.7958 (mp) REVERT: A 451 LEU cc_start: 0.8952 (mt) cc_final: 0.8738 (mt) REVERT: B 187 ASP cc_start: 0.9065 (m-30) cc_final: 0.8847 (m-30) REVERT: B 269 MET cc_start: 0.8988 (tpp) cc_final: 0.8613 (tpp) REVERT: B 291 ASP cc_start: 0.8985 (m-30) cc_final: 0.8692 (p0) REVERT: B 301 MET cc_start: 0.9125 (tmm) cc_final: 0.8794 (tmm) REVERT: B 348 MET cc_start: 0.7555 (mtp) cc_final: 0.7169 (ttm) REVERT: C 235 MET cc_start: 0.8973 (mmp) cc_final: 0.8718 (mmm) REVERT: C 250 MET cc_start: 0.8759 (tmm) cc_final: 0.8532 (tmm) REVERT: C 312 ILE cc_start: 0.9451 (mp) cc_final: 0.9037 (tt) REVERT: C 322 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 382 LEU cc_start: 0.8916 (mt) cc_final: 0.8667 (mt) REVERT: C 419 TYR cc_start: 0.7608 (t80) cc_final: 0.7147 (t80) REVERT: C 427 ASN cc_start: 0.8315 (p0) cc_final: 0.8085 (p0) REVERT: D 50 ASP cc_start: 0.8561 (m-30) cc_final: 0.7927 (p0) REVERT: D 118 ASN cc_start: 0.9527 (m-40) cc_final: 0.9176 (m-40) REVERT: D 160 LEU cc_start: 0.9251 (tp) cc_final: 0.8953 (tt) REVERT: D 270 MET cc_start: 0.8918 (ttm) cc_final: 0.8411 (tmm) REVERT: D 301 MET cc_start: 0.8914 (mtm) cc_final: 0.8522 (mtt) REVERT: E 42 MET cc_start: 0.8381 (ptp) cc_final: 0.7572 (ppp) REVERT: E 92 GLU cc_start: 0.8887 (tt0) cc_final: 0.8429 (tm-30) REVERT: E 167 LYS cc_start: 0.9258 (pttp) cc_final: 0.9027 (pttp) REVERT: E 187 ASP cc_start: 0.8603 (m-30) cc_final: 0.8349 (p0) REVERT: E 301 MET cc_start: 0.8976 (mtm) cc_final: 0.8771 (mtp) REVERT: E 348 MET cc_start: 0.8622 (mmp) cc_final: 0.8147 (mmp) REVERT: E 363 GLU cc_start: 0.9175 (tp30) cc_final: 0.8965 (tp30) REVERT: E 373 LYS cc_start: 0.9583 (mmmt) cc_final: 0.9380 (mmmm) REVERT: F 98 ASP cc_start: 0.7877 (t0) cc_final: 0.7627 (p0) REVERT: F 235 MET cc_start: 0.7431 (mtt) cc_final: 0.6733 (mtp) REVERT: F 391 GLN cc_start: 0.9416 (mt0) cc_final: 0.9133 (mt0) REVERT: F 414 LEU cc_start: 0.9078 (tp) cc_final: 0.8832 (tp) REVERT: G 468 VAL cc_start: 0.6483 (t) cc_final: 0.6281 (t) REVERT: G 512 ASN cc_start: 0.7997 (t160) cc_final: 0.6750 (m110) REVERT: G 537 ASP cc_start: 0.8779 (t0) cc_final: 0.8442 (t0) REVERT: G 568 CYS cc_start: 0.8107 (m) cc_final: 0.7717 (t) REVERT: H 539 LEU cc_start: 0.9239 (mm) cc_final: 0.9012 (pp) REVERT: H 541 HIS cc_start: 0.9008 (m90) cc_final: 0.8761 (m-70) REVERT: H 550 ARG cc_start: 0.9025 (mmp80) cc_final: 0.8731 (mmm160) REVERT: I 489 VAL cc_start: 0.3881 (t) cc_final: 0.3490 (t) REVERT: I 530 ILE cc_start: 0.8860 (tt) cc_final: 0.8633 (pt) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1725 time to fit residues: 98.7189 Evaluate side-chains 279 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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: 6.9990 chunk 258 optimal weight: 5.9990 chunk 257 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 40.0000 chunk 201 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 192 optimal weight: 30.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** C 195 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.073192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.056557 restraints weight = 175696.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.057945 restraints weight = 125307.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.058946 restraints weight = 96304.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.059713 restraints weight = 78770.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.060172 restraints weight = 67471.653| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24908 Z= 0.192 Angle : 1.053 31.249 33783 Z= 0.432 Chirality : 0.042 0.273 3852 Planarity : 0.005 0.194 4422 Dihedral : 7.238 132.948 3554 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 1.25 (0.15), residues: 3066 helix: 1.55 (0.12), residues: 1794 sheet: -0.77 (0.28), residues: 319 loop : 0.22 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 329 TYR 0.029 0.002 TYR D 122 PHE 0.037 0.002 PHE C 166 TRP 0.038 0.002 TRP D 457 HIS 0.006 0.001 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (24900) covalent geometry : angle 1.05288 / 0.43 (33777) SS BOND : bond 0.00877 / 0.45 ( 3) SS BOND : angle 1.56421 / 0.78 ( 6) hydrogen bonds : bond 0.03359 / 2.30 ( 1466) hydrogen bonds : angle 4.50769 / 3.31 ( 4128) Misc. bond : bond 0.00200 / 0.10 ( 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 352 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.949 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: A 58 ASP cc_start: 0.9164 (m-30) cc_final: 0.8622 (p0) REVERT: A 291 ASP cc_start: 0.8887 (m-30) cc_final: 0.8245 (p0) REVERT: A 451 LEU cc_start: 0.8972 (mt) cc_final: 0.8746 (mt) REVERT: B 187 ASP cc_start: 0.9008 (m-30) cc_final: 0.8782 (m-30) REVERT: B 269 MET cc_start: 0.8956 (tpp) cc_final: 0.8569 (tpp) REVERT: B 291 ASP cc_start: 0.8995 (m-30) cc_final: 0.8691 (p0) REVERT: B 301 MET cc_start: 0.9116 (tmm) cc_final: 0.8791 (tmm) REVERT: B 348 MET cc_start: 0.7534 (mtp) cc_final: 0.7178 (ttm) REVERT: C 235 MET cc_start: 0.8960 (mmp) cc_final: 0.8691 (mmm) REVERT: C 250 MET cc_start: 0.8767 (tmm) cc_final: 0.8539 (tmm) REVERT: C 312 ILE cc_start: 0.9440 (mp) cc_final: 0.9036 (tt) REVERT: C 322 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 382 LEU cc_start: 0.8956 (mt) cc_final: 0.8715 (mt) REVERT: C 392 ARG cc_start: 0.9041 (tmt170) cc_final: 0.8810 (tpt-90) REVERT: C 419 TYR cc_start: 0.7550 (t80) cc_final: 0.7015 (t80) REVERT: C 427 ASN cc_start: 0.8355 (p0) cc_final: 0.8141 (p0) REVERT: D 50 ASP cc_start: 0.8483 (m-30) cc_final: 0.7828 (p0) REVERT: D 118 ASN cc_start: 0.9568 (m-40) cc_final: 0.9217 (m-40) REVERT: D 160 LEU cc_start: 0.9266 (tp) cc_final: 0.9006 (tt) REVERT: D 301 MET cc_start: 0.8959 (mtm) cc_final: 0.8547 (mtt) REVERT: D 348 MET cc_start: 0.8571 (tpp) cc_final: 0.8110 (tpp) REVERT: E 42 MET cc_start: 0.8375 (ptp) cc_final: 0.7613 (ppp) REVERT: E 92 GLU cc_start: 0.8853 (tt0) cc_final: 0.8403 (tm-30) REVERT: E 167 LYS cc_start: 0.9283 (pttp) cc_final: 0.9082 (pttp) REVERT: E 187 ASP cc_start: 0.8622 (m-30) cc_final: 0.8368 (p0) REVERT: E 301 MET cc_start: 0.8975 (mtm) cc_final: 0.8696 (ptp) REVERT: E 348 MET cc_start: 0.8666 (mmp) cc_final: 0.8151 (mmp) REVERT: E 373 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9385 (mmmm) REVERT: F 41 LEU cc_start: 0.9172 (mt) cc_final: 0.8844 (mt) REVERT: F 98 ASP cc_start: 0.7919 (t0) cc_final: 0.7651 (p0) REVERT: F 235 MET cc_start: 0.7367 (mtt) cc_final: 0.6632 (mtp) REVERT: F 263 MET cc_start: 0.7198 (mpp) cc_final: 0.6911 (mpp) REVERT: F 391 GLN cc_start: 0.9400 (mt0) cc_final: 0.9099 (mt0) REVERT: G 537 ASP cc_start: 0.8764 (t0) cc_final: 0.8430 (t0) REVERT: G 568 CYS cc_start: 0.8219 (m) cc_final: 0.7849 (t) REVERT: H 539 LEU cc_start: 0.9241 (mm) cc_final: 0.9021 (pp) REVERT: H 541 HIS cc_start: 0.9035 (m90) cc_final: 0.8804 (m-70) REVERT: H 550 ARG cc_start: 0.9035 (mmp80) cc_final: 0.8744 (mmm160) REVERT: I 530 ILE cc_start: 0.8848 (tt) cc_final: 0.8621 (pt) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1664 time to fit residues: 93.2611 Evaluate side-chains 270 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 5.9990 chunk 295 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 171 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.073967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.057391 restraints weight = 175355.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.058798 restraints weight = 124117.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.059790 restraints weight = 95209.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.060565 restraints weight = 77873.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.061050 restraints weight = 66400.245| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24908 Z= 0.150 Angle : 1.036 31.717 33783 Z= 0.422 Chirality : 0.042 0.318 3852 Planarity : 0.004 0.085 4422 Dihedral : 7.141 131.730 3554 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.28 (0.15), residues: 3066 helix: 1.57 (0.12), residues: 1798 sheet: -0.60 (0.28), residues: 313 loop : 0.15 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 329 TYR 0.027 0.001 TYR D 122 PHE 0.026 0.002 PHE B 240 TRP 0.036 0.002 TRP F 48 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24900) covalent geometry : angle 1.03587 / 0.42 (33777) SS BOND : bond 0.01130 / 0.57 ( 3) SS BOND : angle 2.42170 / 1.15 ( 6) hydrogen bonds : bond 0.03301 / 2.27 ( 1466) hydrogen bonds : angle 4.45516 / 3.28 ( 4128) Misc. bond : bond 0.00155 / 0.08 ( 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 351 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.011 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: A 58 ASP cc_start: 0.9139 (m-30) cc_final: 0.8596 (p0) REVERT: A 291 ASP cc_start: 0.8861 (m-30) cc_final: 0.8226 (p0) REVERT: A 416 MET cc_start: 0.8949 (mmt) cc_final: 0.8494 (mmm) REVERT: A 438 ILE cc_start: 0.8389 (mp) cc_final: 0.7512 (mp) REVERT: A 451 LEU cc_start: 0.8966 (mt) cc_final: 0.8728 (mt) REVERT: B 187 ASP cc_start: 0.8991 (m-30) cc_final: 0.8749 (m-30) REVERT: B 225 ASP cc_start: 0.7578 (m-30) cc_final: 0.7302 (m-30) REVERT: B 269 MET cc_start: 0.8946 (tpp) cc_final: 0.8557 (tpp) REVERT: B 291 ASP cc_start: 0.8856 (m-30) cc_final: 0.8621 (p0) REVERT: B 301 MET cc_start: 0.9120 (tmm) cc_final: 0.8648 (ppp) REVERT: B 348 MET cc_start: 0.7429 (mtp) cc_final: 0.7149 (ttm) REVERT: C 235 MET cc_start: 0.8931 (mmp) cc_final: 0.8638 (mmm) REVERT: C 250 MET cc_start: 0.8785 (tmm) cc_final: 0.8549 (tmm) REVERT: C 312 ILE cc_start: 0.9385 (mp) cc_final: 0.8937 (tt) REVERT: C 322 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 382 LEU cc_start: 0.8967 (mt) cc_final: 0.8748 (mt) REVERT: C 392 ARG cc_start: 0.9042 (tmt170) cc_final: 0.8792 (tpt-90) REVERT: C 419 TYR cc_start: 0.7546 (t80) cc_final: 0.7025 (t80) REVERT: C 427 ASN cc_start: 0.8432 (p0) cc_final: 0.8210 (p0) REVERT: D 50 ASP cc_start: 0.8515 (m-30) cc_final: 0.7838 (p0) REVERT: D 72 MET cc_start: 0.9053 (pmm) cc_final: 0.8568 (pmm) REVERT: D 118 ASN cc_start: 0.9539 (m-40) cc_final: 0.9167 (m-40) REVERT: D 160 LEU cc_start: 0.9275 (tp) cc_final: 0.9032 (tt) REVERT: D 301 MET cc_start: 0.8907 (mtm) cc_final: 0.8514 (mtt) REVERT: D 348 MET cc_start: 0.8577 (tpp) cc_final: 0.8176 (tpp) REVERT: E 42 MET cc_start: 0.8430 (ptp) cc_final: 0.7650 (ppp) REVERT: E 92 GLU cc_start: 0.8840 (tt0) cc_final: 0.8394 (tm-30) REVERT: E 167 LYS cc_start: 0.9282 (pttp) cc_final: 0.9061 (pttp) REVERT: E 187 ASP cc_start: 0.8602 (m-30) cc_final: 0.8365 (p0) REVERT: E 263 MET cc_start: 0.8419 (mtp) cc_final: 0.7992 (mpp) REVERT: E 348 MET cc_start: 0.8639 (mmp) cc_final: 0.8106 (mmp) REVERT: E 363 GLU cc_start: 0.9135 (tp30) cc_final: 0.8917 (tp30) REVERT: E 373 LYS cc_start: 0.9579 (mmmt) cc_final: 0.9365 (mmmm) REVERT: F 98 ASP cc_start: 0.7901 (t0) cc_final: 0.7653 (p0) REVERT: F 235 MET cc_start: 0.7352 (mtt) cc_final: 0.6439 (mtp) REVERT: F 391 GLN cc_start: 0.9394 (mt0) cc_final: 0.9019 (mt0) REVERT: G 537 ASP cc_start: 0.8735 (t0) cc_final: 0.8410 (t0) REVERT: G 568 CYS cc_start: 0.8018 (m) cc_final: 0.7732 (t) REVERT: H 539 LEU cc_start: 0.9248 (mm) cc_final: 0.9035 (pp) REVERT: H 541 HIS cc_start: 0.9063 (m90) cc_final: 0.8846 (m-70) REVERT: H 550 ARG cc_start: 0.9040 (mmp80) cc_final: 0.8743 (mmm160) REVERT: I 521 MET cc_start: 0.7302 (ppp) cc_final: 0.7063 (pmm) REVERT: I 530 ILE cc_start: 0.8834 (tt) cc_final: 0.8613 (pt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1658 time to fit residues: 93.2418 Evaluate side-chains 273 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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: 5.9990 chunk 186 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.074037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.057514 restraints weight = 174810.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.058920 restraints weight = 123791.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.059926 restraints weight = 95109.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060664 restraints weight = 77784.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.061162 restraints weight = 66885.332| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24908 Z= 0.150 Angle : 1.042 31.401 33783 Z= 0.424 Chirality : 0.042 0.272 3852 Planarity : 0.004 0.072 4422 Dihedral : 7.115 131.970 3554 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.25 (0.15), residues: 3066 helix: 1.55 (0.12), residues: 1799 sheet: -0.62 (0.28), residues: 314 loop : 0.12 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 442 TYR 0.027 0.001 TYR D 122 PHE 0.020 0.002 PHE B 240 TRP 0.046 0.002 TRP E 48 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24900) covalent geometry : angle 1.04204 / 0.42 (33777) SS BOND : bond 0.01030 / 0.52 ( 3) SS BOND : angle 2.35397 / 1.17 ( 6) hydrogen bonds : bond 0.03290 / 2.28 ( 1466) hydrogen bonds : angle 4.49030 / 3.29 ( 4128) Misc. bond : bond 0.00144 / 0.08 ( 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 348 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.994 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: A 38 LEU cc_start: 0.8846 (pp) cc_final: 0.8608 (pp) REVERT: A 58 ASP cc_start: 0.9098 (m-30) cc_final: 0.8550 (p0) REVERT: A 84 LEU cc_start: 0.9284 (pp) cc_final: 0.8974 (mt) REVERT: A 291 ASP cc_start: 0.8885 (m-30) cc_final: 0.8260 (p0) REVERT: A 416 MET cc_start: 0.8861 (mmt) cc_final: 0.8452 (mmm) REVERT: A 438 ILE cc_start: 0.8285 (mp) cc_final: 0.7441 (mp) REVERT: A 451 LEU cc_start: 0.8933 (mt) cc_final: 0.8703 (mt) REVERT: B 42 MET cc_start: 0.8209 (mtp) cc_final: 0.7916 (mtp) REVERT: B 72 MET cc_start: 0.8727 (mtt) cc_final: 0.8270 (mtp) REVERT: B 82 ILE cc_start: 0.8338 (mt) cc_final: 0.8095 (mt) REVERT: B 187 ASP cc_start: 0.8937 (m-30) cc_final: 0.8696 (m-30) REVERT: B 225 ASP cc_start: 0.7417 (m-30) cc_final: 0.7215 (m-30) REVERT: B 269 MET cc_start: 0.8866 (tpp) cc_final: 0.8490 (tpp) REVERT: B 291 ASP cc_start: 0.8712 (m-30) cc_final: 0.8507 (p0) REVERT: B 301 MET cc_start: 0.9092 (tmm) cc_final: 0.8660 (ppp) REVERT: C 167 LYS cc_start: 0.9418 (mtmm) cc_final: 0.9204 (mtmm) REVERT: C 235 MET cc_start: 0.8809 (mmp) cc_final: 0.8570 (mmm) REVERT: C 250 MET cc_start: 0.8718 (tmm) cc_final: 0.8487 (tmm) REVERT: C 312 ILE cc_start: 0.9274 (mp) cc_final: 0.8793 (tt) REVERT: C 322 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 392 ARG cc_start: 0.8934 (tmt170) cc_final: 0.8725 (tpt-90) REVERT: D 50 ASP cc_start: 0.8470 (m-30) cc_final: 0.7813 (p0) REVERT: D 72 MET cc_start: 0.8994 (pmm) cc_final: 0.8537 (pmm) REVERT: D 118 ASN cc_start: 0.9507 (m-40) cc_final: 0.9237 (m-40) REVERT: D 160 LEU cc_start: 0.9215 (tp) cc_final: 0.8961 (tt) REVERT: D 301 MET cc_start: 0.8748 (mtm) cc_final: 0.8391 (mtt) REVERT: D 348 MET cc_start: 0.8454 (tpp) cc_final: 0.8128 (tpp) REVERT: E 42 MET cc_start: 0.8357 (ptp) cc_final: 0.7638 (ppp) REVERT: E 92 GLU cc_start: 0.8800 (tt0) cc_final: 0.8383 (tm-30) REVERT: E 167 LYS cc_start: 0.9266 (pttp) cc_final: 0.9045 (pttp) REVERT: E 187 ASP cc_start: 0.8574 (m-30) cc_final: 0.8311 (p0) REVERT: E 263 MET cc_start: 0.8276 (mtp) cc_final: 0.7933 (mpp) REVERT: E 348 MET cc_start: 0.8541 (mmp) cc_final: 0.8067 (mmp) REVERT: E 363 GLU cc_start: 0.9124 (tp30) cc_final: 0.8897 (tp30) REVERT: E 373 LYS cc_start: 0.9551 (mmmt) cc_final: 0.9333 (mmmm) REVERT: F 98 ASP cc_start: 0.7853 (t0) cc_final: 0.7605 (p0) REVERT: F 227 ILE cc_start: 0.8351 (tp) cc_final: 0.7988 (tp) REVERT: F 235 MET cc_start: 0.7352 (mtt) cc_final: 0.6580 (mtp) REVERT: F 341 MET cc_start: 0.8596 (tpt) cc_final: 0.8159 (tpp) REVERT: F 391 GLN cc_start: 0.9382 (mt0) cc_final: 0.9015 (mt0) REVERT: G 537 ASP cc_start: 0.8751 (t0) cc_final: 0.8432 (t0) REVERT: G 568 CYS cc_start: 0.7955 (m) cc_final: 0.7718 (t) REVERT: H 539 LEU cc_start: 0.9252 (mm) cc_final: 0.9038 (pp) REVERT: H 541 HIS cc_start: 0.9053 (m90) cc_final: 0.8832 (m-70) REVERT: H 550 ARG cc_start: 0.9052 (mmp80) cc_final: 0.8734 (mmm160) REVERT: I 521 MET cc_start: 0.7290 (ppp) cc_final: 0.7063 (pmm) REVERT: I 530 ILE cc_start: 0.8827 (tt) cc_final: 0.8602 (pt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1691 time to fit residues: 93.8314 Evaluate side-chains 263 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 4.9990 chunk 296 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.072322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.056044 restraints weight = 179695.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.057322 restraints weight = 127747.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.058323 restraints weight = 98990.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.059036 restraints weight = 81146.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.059565 restraints weight = 69604.394| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24908 Z= 0.197 Angle : 1.071 32.625 33783 Z= 0.443 Chirality : 0.042 0.224 3852 Planarity : 0.005 0.168 4422 Dihedral : 7.327 135.064 3554 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.06 (0.15), residues: 3066 helix: 1.40 (0.12), residues: 1800 sheet: -0.76 (0.28), residues: 316 loop : 0.06 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 442 TYR 0.029 0.002 TYR D 122 PHE 0.023 0.002 PHE B 60 TRP 0.033 0.002 TRP F 48 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (24900) covalent geometry : angle 1.07083 / 0.44 (33777) SS BOND : bond 0.01065 / 0.54 ( 3) SS BOND : angle 2.42152 / 1.16 ( 6) hydrogen bonds : bond 0.03433 / 2.36 ( 1466) hydrogen bonds : angle 4.58893 / 3.37 ( 4128) Misc. bond : bond 0.00179 / 0.09 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5252.28 seconds wall clock time: 91 minutes 18.90 seconds (5478.90 seconds total)