Starting phenix.real_space_refine on Mon Jan 13 13:06:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eco_47923/01_2025/9eco_47923_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eco_47923/01_2025/9eco_47923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eco_47923/01_2025/9eco_47923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eco_47923/01_2025/9eco_47923.map" model { file = "/net/cci-nas-00/data/ceres_data/9eco_47923/01_2025/9eco_47923_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eco_47923/01_2025/9eco_47923_trim.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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: 9 Type Number sf(0) Gaussians Al 5 5.89 5 P 23 5.49 5 Mg 5 5.21 5 S 94 5.16 5 C 14494 2.51 5 N 4149 2.21 5 O 4717 1.98 5 F 20 1.80 5 H 23184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 46691 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6980 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "B" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6979 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 6980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6980 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "D" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6979 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 6980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6980 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "F" Number of atoms: 6980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6980 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "G" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2116 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "H" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2116 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "M" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 416 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'ALF': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 19.67, per 1000 atoms: 0.42 Number of scatterers: 46691 At special positions: 0 Unit cell: (122.01, 150.23, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 94 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 4717 8.00 N 4149 7.00 C 14494 6.00 H 23184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS G 568 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS H 568 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 6 sheets defined 63.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.589A pdb=" N GLY A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.629A pdb=" N THR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.543A pdb=" N TYR A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 174 removed outlier: 3.840A pdb=" N ASN A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.916A pdb=" N LYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.686A pdb=" N ILE A 268 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.702A pdb=" N THR A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.954A pdb=" N ARG A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 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 387 through 392 removed outlier: 4.150A pdb=" N GLN A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.702A pdb=" N LEU A 402 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.707A pdb=" N ASP A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.987A 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 Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.125A pdb=" N PHE B 60 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 95 through 101 removed outlier: 4.323A pdb=" N SER B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.808A pdb=" N SER B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.606A pdb=" N ASP B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 173 Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.680A pdb=" N LYS B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) 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 removed outlier: 3.535A pdb=" N ILE B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) 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 356 through 376 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.862A pdb=" N GLN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 392' Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.555A pdb=" N LEU B 402 " --> pdb=" O ASN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.515A pdb=" N GLU C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.857A pdb=" N ARG C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.569A pdb=" N GLY C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.628A pdb=" N LEU C 106 " --> pdb=" O GLY C 102 " (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 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 removed outlier: 3.529A pdb=" N ILE C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 387 through 392 removed outlier: 3.530A pdb=" N ARG C 392 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.597A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.741A pdb=" N PHE D 60 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 118 through 148 Processing helix chain 'D' and resid 153 through 172 Processing helix chain 'D' and resid 182 through 199 removed outlier: 3.578A pdb=" N GLN D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.105A pdb=" N LYS D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) 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 356 through 376 Processing helix chain 'D' and resid 387 through 392 removed outlier: 3.509A pdb=" N ARG D 392 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.633A pdb=" N LEU D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 420 through 424 Processing helix chain 'E' and resid 30 through 44 removed outlier: 3.590A pdb=" N GLU E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 53 removed outlier: 3.525A pdb=" N VAL E 51 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.065A pdb=" N PHE E 60 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 85 through 95 Processing helix chain 'E' and resid 95 through 101 removed outlier: 4.449A pdb=" N SER E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 118 through 148 removed outlier: 3.606A pdb=" N TYR E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 171 removed outlier: 3.559A pdb=" N LEU E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 199 Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.730A pdb=" N LYS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 251 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 280 through 287 removed outlier: 3.757A pdb=" N ILE E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) 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 356 through 376 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.582A pdb=" N ARG E 392 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.673A pdb=" N LEU E 402 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 420 through 424 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 47 through 55 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 102 through 113 removed outlier: 3.629A pdb=" N SER F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 148 removed outlier: 3.812A pdb=" N TYR F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 171 Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.610A pdb=" N VAL F 185 " --> pdb=" O ASN F 181 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.538A pdb=" N LYS F 216 " --> pdb=" O ASP F 212 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) 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 removed outlier: 3.702A pdb=" N ILE F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) 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 356 through 376 Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 398 through 402 removed outlier: 3.917A pdb=" N LEU F 402 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 420 through 425 removed outlier: 4.231A pdb=" N TYR F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 458 Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 462 through 468 Processing helix chain 'G' and resid 475 through 479 removed outlier: 3.605A pdb=" N LYS G 478 " --> pdb=" O ASP G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 481 through 495 removed outlier: 3.607A pdb=" N PHE G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 487 " --> pdb=" O GLY G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 507 removed outlier: 4.108A pdb=" N TYR G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 522 Processing helix chain 'G' and resid 528 through 562 Processing helix chain 'G' and resid 564 through 581 Processing helix chain 'H' and resid 450 through 461 removed outlier: 3.548A pdb=" N LEU H 454 " --> pdb=" O THR H 450 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE H 455 " --> pdb=" O MET H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 468 Processing helix chain 'H' and resid 475 through 479 removed outlier: 3.576A pdb=" N LEU H 479 " --> pdb=" O GLU H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 495 removed outlier: 4.115A pdb=" N PHE H 485 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 506 Processing helix chain 'H' and resid 512 through 522 Processing helix chain 'H' and resid 528 through 562 Processing helix chain 'H' and resid 564 through 574 Processing helix chain 'H' and resid 574 through 579 removed outlier: 4.267A pdb=" N LEU H 578 " --> pdb=" O LEU H 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.420A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLN B 384 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.420A 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: 6.431A pdb=" N VAL B 229 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 226 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N MET B 416 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 228 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 418 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA B 230 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ARG B 420 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 312 removed outlier: 5.969A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 340 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU A 382 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A 342 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 227 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N SER A 383 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 229 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 226 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N MET A 416 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 228 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 418 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA A 230 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 447 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 181 removed outlier: 6.468A pdb=" N VAL C 256 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASP C 313 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE C 340 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU C 382 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 342 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 227 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 226 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET C 416 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY C 447 " --> pdb=" O ILE C 438 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 180 through 181 removed outlier: 6.406A pdb=" N ILE D 227 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER D 383 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL D 229 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 226 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N MET D 416 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 228 " --> pdb=" O MET D 416 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 418 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA D 230 " --> pdb=" O ILE D 418 " (cutoff:3.500A) removed outlier: 6.294A 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: 6.347A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU E 382 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE E 342 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU E 226 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET E 416 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE E 228 " --> pdb=" O MET E 416 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 418 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA E 230 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 310 through 313 removed outlier: 6.300A pdb=" N VAL F 256 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASP F 313 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 258 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU F 257 " --> pdb=" O MET F 341 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP F 343 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE F 259 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE F 227 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER F 383 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL F 229 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU F 226 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET F 416 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE F 228 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE F 418 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA F 230 " --> pdb=" O ILE F 418 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 3921 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: 15.45 Time building geometry restraints manager: 12.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 23178 1.03 - 1.23: 179 1.23 - 1.43: 9499 1.43 - 1.62: 13986 1.62 - 1.82: 198 Bond restraints: 47040 Sorted by residual: bond pdb=" F1 ALF A 501 " pdb="AL ALF A 501 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.684 1.798 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" F3 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.684 1.796 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" F1 ALF C1004 " pdb="AL ALF C1004 " ideal model delta sigma weight residual 1.684 1.796 -0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 47035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.23: 85080 14.23 - 28.46: 20 28.46 - 42.69: 0 42.69 - 56.92: 0 56.92 - 71.15: 10 Bond angle restraints: 85110 Sorted by residual: angle pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " pdb=" F2 ALF E1002 " ideal model delta sigma weight residual 108.68 179.83 -71.15 3.00e+00 1.11e-01 5.62e+02 angle pdb=" F1 ALF C1004 " pdb="AL ALF C1004 " pdb=" F2 ALF C1004 " ideal model delta sigma weight residual 108.68 179.78 -71.10 3.00e+00 1.11e-01 5.62e+02 angle pdb=" F1 ALF C1002 " pdb="AL ALF C1002 " pdb=" F2 ALF C1002 " ideal model delta sigma weight residual 108.68 179.45 -70.77 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " pdb=" F2 ALF F1002 " ideal model delta sigma weight residual 108.68 179.35 -70.67 3.00e+00 1.11e-01 5.55e+02 angle pdb=" F1 ALF A 501 " pdb="AL ALF A 501 " pdb=" F2 ALF A 501 " ideal model delta sigma weight residual 108.68 179.13 -70.45 3.00e+00 1.11e-01 5.52e+02 ... (remaining 85105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.82: 21045 30.82 - 61.64: 783 61.64 - 92.45: 25 92.45 - 123.27: 2 123.27 - 154.09: 2 Dihedral angle restraints: 21857 sinusoidal: 12427 harmonic: 9430 Sorted by residual: dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 94.09 -154.09 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PA ADP D1001 " pdb=" PB ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 69.67 -129.67 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" O2A ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PA ADP C1001 " pdb=" PB ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 56.75 -116.75 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 21854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2489 0.029 - 0.058: 759 0.058 - 0.087: 238 0.087 - 0.115: 149 0.115 - 0.144: 47 Chirality restraints: 3682 Sorted by residual: chirality pdb=" CA VAL D 377 " pdb=" N VAL D 377 " pdb=" C VAL D 377 " pdb=" CB VAL D 377 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CG LEU A 38 " pdb=" CB LEU A 38 " pdb=" CD1 LEU A 38 " pdb=" CD2 LEU A 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL E 279 " pdb=" N VAL E 279 " pdb=" C VAL E 279 " pdb=" CB VAL E 279 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 3679 not shown) Planarity restraints: 7064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 486 " 0.258 9.50e-02 1.11e+02 8.63e-02 8.01e+00 pdb=" NE ARG H 486 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG H 486 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG H 486 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 486 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG H 486 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG H 486 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG H 486 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG H 486 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 118 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C ASN D 118 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN D 118 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE D 119 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 485 " 0.010 2.00e-02 2.50e+03 1.00e-02 3.03e+00 pdb=" CG PHE H 485 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 485 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE H 485 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE H 485 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE H 485 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 485 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE H 485 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE H 485 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE H 485 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE H 485 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE H 485 " -0.001 2.00e-02 2.50e+03 ... (remaining 7061 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.04: 423 2.04 - 2.68: 70839 2.68 - 3.32: 135766 3.32 - 3.96: 171199 3.96 - 4.60: 271661 Nonbonded interactions: 649888 Sorted by model distance: nonbonded pdb=" OE1 GLU C 292 " pdb=" H GLU C 292 " model vdw 1.395 2.450 nonbonded pdb=" O GLN A 281 " pdb=" H ILE A 284 " model vdw 1.546 2.450 nonbonded pdb=" OG SER E 405 " pdb="HH12 ARG F 387 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP H 527 " pdb=" H ILE H 530 " model vdw 1.599 2.450 nonbonded pdb=" O GLN C 252 " pdb=" HZ1 LYS C 307 " model vdw 1.600 2.450 ... (remaining 649883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 102 or (resid 103 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 104 through 471)) selection = (chain 'B' and resid 24 through 471) selection = (chain 'C' and (resid 24 through 102 or (resid 103 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 104 through 471)) selection = (chain 'D' and resid 24 through 471) selection = (chain 'E' and (resid 24 through 102 or (resid 103 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 104 through 471)) selection = (chain 'F' and (resid 24 through 102 or (resid 103 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 104 through 471)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.630 Extract box with map and model: 1.510 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 77.900 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.005 0.115 23856 Z= 0.275 Angle : 1.423 71.151 32357 Z= 0.509 Chirality : 0.038 0.144 3682 Planarity : 0.004 0.113 4236 Dihedral : 14.316 154.091 9154 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Rotamer: Outliers : 1.55 % Allowed : 14.34 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2938 helix: 2.85 (0.13), residues: 1582 sheet: -0.24 (0.31), residues: 310 loop : -0.53 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 48 HIS 0.004 0.001 HIS G 541 PHE 0.030 0.001 PHE H 485 TYR 0.008 0.001 TYR D 468 ARG 0.006 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 2.932 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 172 ARG cc_start: 0.8304 (ttp-170) cc_final: 0.7399 (mmp-170) REVERT: A 463 TYR cc_start: 0.7942 (t80) cc_final: 0.7633 (t80) REVERT: C 42 MET cc_start: 0.6840 (tmm) cc_final: 0.6008 (mtp) REVERT: C 71 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: D 135 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7127 (mtp) REVERT: D 426 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8016 (pp20) REVERT: G 473 ASN cc_start: 0.6751 (m-40) cc_final: 0.6520 (p0) REVERT: G 517 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: H 458 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8335 (tm) REVERT: H 492 CYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7242 (m) outliers start: 39 outliers final: 30 residues processed: 187 average time/residue: 2.0015 time to fit residues: 442.1553 Evaluate side-chains 184 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 492 CYS Chi-restraints excluded: chain H residue 554 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 454 ASN D 195 GLN D 199 GLN F 281 GLN F 386 ASN H 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.114380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066662 restraints weight = 162404.441| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.83 r_work: 0.2981 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23856 Z= 0.282 Angle : 1.006 30.912 32357 Z= 0.403 Chirality : 0.040 0.182 3682 Planarity : 0.004 0.046 4236 Dihedral : 8.755 142.769 3486 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 1.79 % Allowed : 14.10 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2938 helix: 2.72 (0.13), residues: 1635 sheet: -0.47 (0.30), residues: 313 loop : -0.78 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.004 0.001 HIS A 334 PHE 0.013 0.001 PHE H 485 TYR 0.006 0.001 TYR D 424 ARG 0.006 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 2.945 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 109 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7342 (tm) REVERT: A 172 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7189 (mmp80) REVERT: A 272 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.9105 (p) REVERT: A 463 TYR cc_start: 0.8055 (t80) cc_final: 0.7755 (t80) REVERT: C 42 MET cc_start: 0.6634 (tmm) cc_final: 0.5792 (mtp) REVERT: C 166 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: D 112 ASN cc_start: 0.4787 (OUTLIER) cc_final: 0.4416 (m110) REVERT: G 473 ASN cc_start: 0.6836 (m-40) cc_final: 0.6585 (p0) REVERT: G 517 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6747 (tm-30) outliers start: 45 outliers final: 22 residues processed: 192 average time/residue: 2.1497 time to fit residues: 483.4130 Evaluate side-chains 173 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 554 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 284 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN C 140 ASN D 195 GLN D 199 GLN D 252 GLN E 45 ASN E 140 ASN F 386 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.113380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065293 restraints weight = 164596.512| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.65 r_work: 0.2966 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 23856 Z= 0.391 Angle : 1.016 32.280 32357 Z= 0.409 Chirality : 0.041 0.161 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.801 147.531 3448 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 2.62 % Allowed : 13.86 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.16), residues: 2938 helix: 2.55 (0.13), residues: 1642 sheet: -0.66 (0.30), residues: 312 loop : -1.03 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 48 HIS 0.004 0.001 HIS A 334 PHE 0.015 0.001 PHE C 460 TYR 0.008 0.001 TYR B 61 ARG 0.014 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 2.911 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 109 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7465 (tm) REVERT: A 172 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.7238 (mmp80) REVERT: A 272 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.9112 (p) REVERT: B 72 MET cc_start: 0.8370 (ttp) cc_final: 0.8151 (mtp) REVERT: B 332 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8289 (ptp-110) REVERT: C 42 MET cc_start: 0.6695 (tmm) cc_final: 0.5988 (mtp) REVERT: C 166 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: D 50 ASP cc_start: 0.9011 (m-30) cc_final: 0.8798 (m-30) REVERT: G 473 ASN cc_start: 0.6762 (m-40) cc_final: 0.6521 (p0) REVERT: G 517 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6758 (tm-30) outliers start: 66 outliers final: 40 residues processed: 214 average time/residue: 2.1695 time to fit residues: 550.4597 Evaluate side-chains 193 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 507 TYR Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 153 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 262 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 151 optimal weight: 0.0020 chunk 137 optimal weight: 40.0000 chunk 53 optimal weight: 8.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN C 140 ASN D 252 GLN F 376 ASN F 386 ASN ** H 490 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 = 0.4150 r_free = 0.4150 target = 0.114799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067129 restraints weight = 163026.493| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.80 r_work: 0.3003 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23856 Z= 0.171 Angle : 0.982 30.557 32357 Z= 0.383 Chirality : 0.039 0.141 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.271 134.490 3446 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 1.79 % Allowed : 15.17 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 2938 helix: 2.76 (0.13), residues: 1635 sheet: -0.65 (0.29), residues: 315 loop : -0.92 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 48 HIS 0.005 0.001 HIS F 65 PHE 0.016 0.001 PHE H 485 TYR 0.008 0.001 TYR D 122 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 2.945 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 109 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7473 (tm) REVERT: A 172 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.7220 (mmp80) REVERT: A 235 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8319 (tpt) REVERT: A 272 SER cc_start: 0.9373 (OUTLIER) cc_final: 0.9108 (p) REVERT: B 72 MET cc_start: 0.8341 (ttp) cc_final: 0.8131 (mtp) REVERT: B 170 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6160 (pp20) REVERT: B 373 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8941 (ttpt) REVERT: C 42 MET cc_start: 0.6640 (tmm) cc_final: 0.5932 (mtp) REVERT: C 166 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7048 (m-80) REVERT: G 517 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: H 550 ARG cc_start: 0.8210 (tpm170) cc_final: 0.7981 (tpm170) outliers start: 45 outliers final: 26 residues processed: 186 average time/residue: 2.1524 time to fit residues: 469.9130 Evaluate side-chains 181 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain G residue 473 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN F 45 ASN F 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.113720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065802 restraints weight = 162917.892| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.63 r_work: 0.2978 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23856 Z= 0.293 Angle : 0.995 31.538 32357 Z= 0.392 Chirality : 0.040 0.152 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.404 143.355 3442 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 2.03 % Allowed : 14.89 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.16), residues: 2938 helix: 2.66 (0.13), residues: 1645 sheet: -0.68 (0.30), residues: 313 loop : -0.99 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.004 0.001 HIS F 65 PHE 0.013 0.001 PHE C 460 TYR 0.009 0.001 TYR F 122 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 2.975 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 109 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7538 (tm) REVERT: A 172 ARG cc_start: 0.8417 (ttp-170) cc_final: 0.7242 (mmp80) REVERT: A 235 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8556 (tpt) REVERT: A 272 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.9125 (p) REVERT: B 72 MET cc_start: 0.8328 (ttp) cc_final: 0.8124 (mtp) REVERT: B 373 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.9004 (ttpt) REVERT: C 166 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: E 468 TYR cc_start: 0.3257 (m-80) cc_final: 0.3043 (m-80) REVERT: G 517 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6802 (tm-30) outliers start: 51 outliers final: 31 residues processed: 196 average time/residue: 2.1715 time to fit residues: 498.3621 Evaluate side-chains 186 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 220 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 285 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 267 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN E 45 ASN F 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.114395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066306 restraints weight = 162265.592| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.74 r_work: 0.2996 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23856 Z= 0.240 Angle : 0.984 30.645 32357 Z= 0.384 Chirality : 0.039 0.145 3682 Planarity : 0.004 0.041 4236 Dihedral : 8.250 143.331 3439 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.63 % Allowed : 15.61 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2938 helix: 2.74 (0.13), residues: 1647 sheet: -0.68 (0.30), residues: 313 loop : -0.97 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 572 HIS 0.004 0.001 HIS D 334 PHE 0.021 0.001 PHE H 485 TYR 0.007 0.001 TYR F 122 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 2.979 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 109 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7518 (tm) REVERT: A 172 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.7384 (mmp-170) REVERT: A 272 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9182 (p) REVERT: B 373 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9054 (ttpt) REVERT: C 166 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: E 468 TYR cc_start: 0.3189 (m-80) cc_final: 0.2988 (m-80) REVERT: G 517 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6796 (tm-30) outliers start: 41 outliers final: 31 residues processed: 189 average time/residue: 2.1158 time to fit residues: 469.6051 Evaluate side-chains 186 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.114139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065930 restraints weight = 162344.772| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.71 r_work: 0.2988 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23856 Z= 0.269 Angle : 0.991 31.031 32357 Z= 0.389 Chirality : 0.039 0.150 3682 Planarity : 0.004 0.041 4236 Dihedral : 8.383 150.568 3439 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 1.75 % Allowed : 15.65 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.16), residues: 2938 helix: 2.73 (0.13), residues: 1641 sheet: -0.72 (0.30), residues: 313 loop : -1.00 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 48 HIS 0.007 0.001 HIS G 541 PHE 0.022 0.001 PHE B 166 TYR 0.011 0.001 TYR F 122 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 3.216 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: A 109 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7540 (tm) REVERT: A 172 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7238 (mmp80) REVERT: A 272 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9183 (p) REVERT: B 373 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9053 (ttpt) REVERT: C 166 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: D 35 GLN cc_start: 0.8865 (mt0) cc_final: 0.8348 (tt0) REVERT: G 517 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: H 518 LYS cc_start: 0.6720 (tmtt) cc_final: 0.6425 (tppt) outliers start: 44 outliers final: 35 residues processed: 190 average time/residue: 2.1041 time to fit residues: 470.4497 Evaluate side-chains 190 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 574 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 251 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN D 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.114131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066131 restraints weight = 162007.362| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.72 r_work: 0.2976 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23856 Z= 0.250 Angle : 0.988 30.892 32357 Z= 0.386 Chirality : 0.039 0.146 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.382 152.360 3439 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 1.63 % Allowed : 15.73 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2938 helix: 2.76 (0.13), residues: 1642 sheet: -0.76 (0.29), residues: 319 loop : -0.96 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 572 HIS 0.005 0.001 HIS G 541 PHE 0.024 0.001 PHE B 166 TYR 0.009 0.001 TYR F 122 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 3.273 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 109 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7572 (tm) REVERT: A 172 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7233 (mmp80) REVERT: A 272 SER cc_start: 0.9445 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 373 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9040 (ttpt) REVERT: C 166 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: E 468 TYR cc_start: 0.3210 (m-80) cc_final: 0.3004 (m-80) REVERT: G 517 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: H 518 LYS cc_start: 0.6718 (tmtt) cc_final: 0.6415 (tppt) outliers start: 41 outliers final: 32 residues processed: 187 average time/residue: 2.1598 time to fit residues: 474.4693 Evaluate side-chains 187 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 517 GLU Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 254 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.113838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065743 restraints weight = 163238.577| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.93 r_work: 0.2970 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23856 Z= 0.254 Angle : 0.989 30.826 32357 Z= 0.386 Chirality : 0.039 0.145 3682 Planarity : 0.004 0.041 4236 Dihedral : 8.460 156.591 3439 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 1.59 % Allowed : 15.85 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.16), residues: 2938 helix: 2.78 (0.13), residues: 1642 sheet: -0.76 (0.29), residues: 319 loop : -0.97 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 294 HIS 0.006 0.001 HIS G 541 PHE 0.028 0.001 PHE B 166 TYR 0.011 0.001 TYR F 122 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 2.961 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 109 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7643 (tm) REVERT: A 172 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.7256 (mmp80) REVERT: A 272 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.9130 (p) REVERT: B 373 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8930 (ttpt) REVERT: C 166 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: H 518 LYS cc_start: 0.6838 (tmtt) cc_final: 0.6562 (tppt) outliers start: 40 outliers final: 33 residues processed: 188 average time/residue: 2.0444 time to fit residues: 453.2922 Evaluate side-chains 187 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 chunk 177 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.114410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066638 restraints weight = 163169.068| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.82 r_work: 0.2999 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23856 Z= 0.170 Angle : 0.980 30.380 32357 Z= 0.379 Chirality : 0.039 0.140 3682 Planarity : 0.003 0.041 4236 Dihedral : 8.241 152.983 3436 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.47 % Allowed : 16.04 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.16), residues: 2938 helix: 2.88 (0.13), residues: 1641 sheet: -0.70 (0.29), residues: 319 loop : -0.92 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 572 HIS 0.005 0.001 HIS G 541 PHE 0.032 0.001 PHE B 166 TYR 0.009 0.001 TYR F 122 ARG 0.003 0.000 ARG E 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 2.992 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 109 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7640 (tm) REVERT: A 172 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.7396 (mmp-170) REVERT: A 272 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9153 (p) REVERT: B 373 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8920 (ttpt) REVERT: C 166 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: H 518 LYS cc_start: 0.6834 (tmtt) cc_final: 0.6554 (tppt) outliers start: 37 outliers final: 31 residues processed: 180 average time/residue: 2.1488 time to fit residues: 459.3347 Evaluate side-chains 183 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 427 ASN Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain H residue 475 ASP Chi-restraints excluded: chain H residue 517 GLU Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 57 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN F 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.112685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064742 restraints weight = 163994.789| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.82 r_work: 0.2942 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 23856 Z= 0.398 Angle : 1.019 32.006 32357 Z= 0.409 Chirality : 0.041 0.170 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.914 165.694 3436 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.89 % Rotamer: Outliers : 1.67 % Allowed : 15.97 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2938 helix: 2.63 (0.13), residues: 1642 sheet: -0.85 (0.29), residues: 318 loop : -1.07 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 294 HIS 0.004 0.001 HIS G 541 PHE 0.023 0.002 PHE H 543 TYR 0.011 0.001 TYR F 122 ARG 0.005 0.000 ARG D 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30555.84 seconds wall clock time: 518 minutes 15.71 seconds (31095.71 seconds total)