Starting phenix.real_space_refine on Fri Dec 27 04:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eco_47923/12_2024/9eco_47923_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eco_47923/12_2024/9eco_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_47923/12_2024/9eco_47923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eco_47923/12_2024/9eco_47923.map" model { file = "/net/cci-nas-00/data/ceres_data/9eco_47923/12_2024/9eco_47923_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eco_47923/12_2024/9eco_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 18.05, per 1000 atoms: 0.39 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: 9.58 Conformation dependent library (CDL) restraints added in 2.7 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: 2.98 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: 15.62 Time building geometry restraints manager: 11.72 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.590 Extract box with map and model: 1.320 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 76.890 Find NCS groups from input model: 1.750 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.670 ------------------------------------------------------------------------------- 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 : 2.837 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: 1.9928 time to fit residues: 440.8901 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 : 2.711 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 2.791 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: 0.7745 (OUTLIER) cc_final: 0.7340 (tm) REVERT: A 172 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.7188 (mmp80) REVERT: A 272 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9080 (p) REVERT: A 463 TYR cc_start: 0.7958 (t80) cc_final: 0.7655 (t80) REVERT: C 42 MET cc_start: 0.6647 (tmm) cc_final: 0.5817 (mtp) REVERT: C 166 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: D 112 ASN cc_start: 0.4819 (OUTLIER) cc_final: 0.4438 (m110) REVERT: G 473 ASN cc_start: 0.6807 (m-40) cc_final: 0.6550 (p0) REVERT: G 517 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6714 (tm-30) outliers start: 45 outliers final: 22 residues processed: 192 average time/residue: 2.1605 time to fit residues: 486.1859 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 : 2.746 ------------------------------------------------------------------------------- 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 146 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23856 Z= 0.333 Angle : 1.002 31.245 32357 Z= 0.399 Chirality : 0.040 0.150 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.625 146.574 3448 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 2.42 % Allowed : 13.82 % Favored : 83.76 % 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: 1.70 (0.16), residues: 2938 helix: 2.64 (0.13), residues: 1642 sheet: -0.63 (0.30), residues: 313 loop : -0.95 (0.19), residues: 983 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 C 460 TYR 0.007 0.001 TYR A 344 ARG 0.017 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 219 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 158 time to evaluate : 2.792 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: 0.7816 (OUTLIER) cc_final: 0.7418 (tm) REVERT: A 172 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.7219 (mmp80) REVERT: A 272 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9067 (p) REVERT: A 301 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7338 (pmm) REVERT: B 72 MET cc_start: 0.8357 (ttp) cc_final: 0.8141 (mtp) REVERT: B 332 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8106 (ptp-110) REVERT: C 42 MET cc_start: 0.6664 (tmm) cc_final: 0.5962 (mtp) REVERT: C 166 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: G 473 ASN cc_start: 0.6733 (m-40) cc_final: 0.6488 (p0) REVERT: G 517 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6726 (tm-30) outliers start: 61 outliers final: 37 residues processed: 210 average time/residue: 2.2014 time to fit residues: 549.4711 Evaluate side-chains 192 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 2.737 ------------------------------------------------------------------------------- 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 4.9990 chunk 199 optimal weight: 0.3980 chunk 137 optimal weight: 20.0000 chunk 29 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 177 optimal weight: 30.0000 chunk 265 optimal weight: 20.0000 chunk 281 optimal weight: 0.0470 chunk 138 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 252 GLN F 386 ASN ** G 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23856 Z= 0.168 Angle : 0.978 30.516 32357 Z= 0.380 Chirality : 0.039 0.141 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.125 132.987 3444 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 1.55 % Allowed : 14.97 % Favored : 83.48 % 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: 1.89 (0.16), residues: 2938 helix: 2.82 (0.13), residues: 1636 sheet: -0.60 (0.30), residues: 315 loop : -0.89 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 48 HIS 0.004 0.001 HIS G 506 PHE 0.015 0.001 PHE H 485 TYR 0.006 0.001 TYR D 311 ARG 0.003 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 192 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 2.773 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: 0.7840 (OUTLIER) cc_final: 0.7455 (tm) REVERT: A 172 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7203 (mmp80) REVERT: A 235 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8243 (tpt) REVERT: A 272 SER cc_start: 0.9362 (OUTLIER) cc_final: 0.9099 (p) REVERT: B 72 MET cc_start: 0.8346 (ttp) cc_final: 0.8127 (mtp) REVERT: B 170 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6194 (pp20) REVERT: B 373 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8899 (ttpt) REVERT: C 166 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: G 517 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: H 550 ARG cc_start: 0.8209 (tpm170) cc_final: 0.7956 (tpm170) outliers start: 39 outliers final: 25 residues processed: 184 average time/residue: 2.0967 time to fit residues: 453.9148 Evaluate side-chains 181 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 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 62 THR 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 234 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN D 252 GLN F 45 ASN F 386 ASN ** G 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 23856 Z= 0.330 Angle : 1.003 31.802 32357 Z= 0.398 Chirality : 0.040 0.168 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.557 144.538 3442 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 2.18 % Allowed : 14.69 % Favored : 83.12 % 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: 1.66 (0.16), residues: 2938 helix: 2.63 (0.13), residues: 1646 sheet: -0.70 (0.30), residues: 313 loop : -1.01 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.005 0.001 HIS G 541 PHE 0.014 0.001 PHE C 460 TYR 0.010 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 206 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 2.759 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: A 109 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7536 (tm) REVERT: A 172 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.7234 (mmp80) REVERT: A 235 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8491 (tpt) REVERT: A 272 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9087 (p) REVERT: B 373 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8914 (ttpt) REVERT: C 166 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: G 517 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6756 (tm-30) outliers start: 55 outliers final: 33 residues processed: 196 average time/residue: 2.1010 time to fit residues: 484.5050 Evaluate side-chains 185 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 2.755 ------------------------------------------------------------------------------- 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 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 250 MET 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 252 GLN 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 62 THR 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 554 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 233 optimal weight: 30.0000 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN F 386 ASN ** G 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 23856 Z= 0.264 Angle : 0.988 30.985 32357 Z= 0.387 Chirality : 0.039 0.149 3682 Planarity : 0.004 0.042 4236 Dihedral : 8.340 143.236 3439 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 1.83 % Allowed : 15.37 % Favored : 82.80 % 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: 1.73 (0.16), residues: 2938 helix: 2.70 (0.13), residues: 1645 sheet: -0.69 (0.30), residues: 313 loop : -0.99 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 48 HIS 0.005 0.001 HIS G 541 PHE 0.019 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 201 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 2.816 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: 0.7876 (OUTLIER) cc_final: 0.7531 (tm) REVERT: A 172 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.7380 (mmp-170) REVERT: A 235 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8497 (tpt) REVERT: A 272 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.9090 (p) REVERT: B 332 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8137 (ptp-110) REVERT: B 373 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8889 (ttpt) REVERT: C 166 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: D 35 GLN cc_start: 0.8844 (mt0) cc_final: 0.8080 (tm130) REVERT: G 517 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6743 (tm-30) outliers start: 46 outliers final: 31 residues processed: 192 average time/residue: 2.1094 time to fit residues: 475.6521 Evaluate side-chains 191 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 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 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 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 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 271 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 280 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23856 Z= 0.169 Angle : 0.976 30.050 32357 Z= 0.377 Chirality : 0.039 0.140 3682 Planarity : 0.003 0.041 4236 Dihedral : 8.014 142.054 3439 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % 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: 1.92 (0.16), residues: 2938 helix: 2.88 (0.13), residues: 1636 sheet: -0.66 (0.30), residues: 315 loop : -0.92 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 572 HIS 0.006 0.001 HIS G 541 PHE 0.022 0.001 PHE G 543 TYR 0.009 0.001 TYR F 122 ARG 0.003 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 198 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7518 (tm) REVERT: A 172 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7357 (mmp-170) REVERT: A 272 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9124 (p) REVERT: B 373 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8870 (ttpt) REVERT: C 166 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: D 35 GLN cc_start: 0.8826 (mt0) cc_final: 0.8316 (tt0) REVERT: G 517 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: H 518 LYS cc_start: 0.6781 (tmtt) cc_final: 0.6487 (tppt) outliers start: 40 outliers final: 29 residues processed: 190 average time/residue: 2.1518 time to fit residues: 480.9118 Evaluate side-chains 187 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 2.734 ------------------------------------------------------------------------------- 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 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 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 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 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 173 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 F 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 23856 Z= 0.307 Angle : 0.997 31.379 32357 Z= 0.392 Chirality : 0.040 0.149 3682 Planarity : 0.004 0.041 4236 Dihedral : 8.410 153.522 3439 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.71 % Allowed : 16.00 % Favored : 82.29 % 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: 1.76 (0.16), residues: 2938 helix: 2.74 (0.13), residues: 1642 sheet: -0.72 (0.30), residues: 313 loop : -0.99 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 572 HIS 0.004 0.001 HIS G 541 PHE 0.024 0.001 PHE H 485 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 196 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 2.843 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: 0.7900 (OUTLIER) cc_final: 0.7548 (tm) REVERT: A 272 SER cc_start: 0.9362 (OUTLIER) cc_final: 0.9106 (p) REVERT: B 373 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8896 (ttpt) REVERT: C 166 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: G 517 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: H 518 LYS cc_start: 0.6715 (tmtt) cc_final: 0.6418 (tppt) outliers start: 43 outliers final: 32 residues processed: 189 average time/residue: 2.0623 time to fit residues: 459.7003 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 : 2.734 ------------------------------------------------------------------------------- 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 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 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 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 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 255 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 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 F 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23856 Z= 0.247 Angle : 0.989 30.707 32357 Z= 0.387 Chirality : 0.039 0.144 3682 Planarity : 0.004 0.041 4236 Dihedral : 8.366 154.140 3439 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 1.51 % Allowed : 16.00 % 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: 1.83 (0.16), residues: 2938 helix: 2.80 (0.13), residues: 1642 sheet: -0.70 (0.29), residues: 313 loop : -0.96 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 572 HIS 0.006 0.001 HIS D 201 PHE 0.020 0.001 PHE H 543 TYR 0.009 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 191 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 2.767 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: 0.7924 (OUTLIER) cc_final: 0.7561 (tm) REVERT: A 172 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.7370 (mmp-170) REVERT: A 272 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9122 (p) REVERT: B 373 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8884 (ttpt) REVERT: C 166 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: D 72 MET cc_start: 0.8715 (tpt) cc_final: 0.8512 (tpt) REVERT: G 517 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: H 518 LYS cc_start: 0.6834 (tmtt) cc_final: 0.6551 (tppt) outliers start: 38 outliers final: 30 residues processed: 184 average time/residue: 2.0389 time to fit residues: 444.2743 Evaluate side-chains 187 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 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 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 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 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 171 optimal weight: 0.5980 chunk 276 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 141 optimal weight: 0.0270 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23856 Z= 0.158 Angle : 0.978 30.264 32357 Z= 0.378 Chirality : 0.039 0.140 3682 Planarity : 0.003 0.041 4236 Dihedral : 8.152 151.099 3439 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 1.43 % Allowed : 16.12 % Favored : 82.45 % 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: 1.97 (0.16), residues: 2938 helix: 2.93 (0.13), residues: 1635 sheet: -0.63 (0.30), residues: 313 loop : -0.91 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 294 HIS 0.005 0.001 HIS G 541 PHE 0.033 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 193 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 2.830 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 41 LEU cc_start: 0.8825 (mm) cc_final: 0.8596 (mt) REVERT: A 109 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7596 (tm) REVERT: A 172 ARG cc_start: 0.8329 (ttp-170) cc_final: 0.7338 (mmp-170) REVERT: A 272 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9134 (p) REVERT: B 373 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8859 (ttpt) REVERT: C 166 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: G 517 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: H 518 LYS cc_start: 0.6832 (tmtt) cc_final: 0.6551 (tppt) outliers start: 36 outliers final: 29 residues processed: 187 average time/residue: 2.0762 time to fit residues: 462.5036 Evaluate side-chains 185 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 2.829 ------------------------------------------------------------------------------- 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 A residue 312 ILE 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 166 PHE 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 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 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 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 183 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.114058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066259 restraints weight = 163152.293| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.88 r_work: 0.2990 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23856 Z= 0.262 Angle : 0.992 30.885 32357 Z= 0.388 Chirality : 0.039 0.147 3682 Planarity : 0.004 0.041 4236 Dihedral : 8.453 158.356 3439 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 1.43 % Allowed : 16.28 % Favored : 82.29 % 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: 2.84 (0.13), residues: 1642 sheet: -0.73 (0.29), residues: 318 loop : -0.96 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 294 HIS 0.004 0.001 HIS G 541 PHE 0.023 0.001 PHE H 543 TYR 0.010 0.001 TYR F 122 ARG 0.004 0.000 ARG E 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9993.35 seconds wall clock time: 172 minutes 20.23 seconds (10340.23 seconds total)