Starting phenix.real_space_refine on Sat Jul 4 07:53:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6m_25719/07_2026/7t6m_25719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6m_25719/07_2026/7t6m_25719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6m_25719/07_2026/7t6m_25719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6m_25719/07_2026/7t6m_25719.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6m_25719/07_2026/7t6m_25719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6m_25719/07_2026/7t6m_25719.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.081 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 12648 2.51 5 N 3284 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.78, per 1000 atoms: 0.19 Number of scatterers: 19600 At special positions: 0 Unit cell: (120.84, 119.78, 120.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 3516 8.00 N 3284 7.00 C 12648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 622.6 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 8 sheets defined 66.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.558A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.812A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.744A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.722A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.550A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.664A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.263A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.926A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.561A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.537A pdb=" N ILE A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.547A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.791A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.579A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.589A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 4.297A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.923A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.698A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.963A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.620A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.811A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.741A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.713A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.559A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.517A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.172A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.892A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.561A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.539A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.548A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.790A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.585A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 4.297A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.925A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.698A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.963A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.654A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.527A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.810A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.745A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.719A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.558A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.766A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.447A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.918A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.562A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.553A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.543A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.803A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.553A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.585A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 4.298A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.936A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.698A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.963A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.533A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.810A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.737A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.716A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.550A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.663A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.263A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.925A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.562A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.539A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.548A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.787A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.583A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 4.303A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 511 removed outlier: 4.925A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.696A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.962A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 Processing helix chain 'D' and resid 620 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.786A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.786A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.788A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.788A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1054 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3116 1.31 - 1.43: 5435 1.43 - 1.56: 11244 1.56 - 1.68: 25 1.68 - 1.81: 228 Bond restraints: 20048 Sorted by residual: bond pdb=" C1A PIO B1001 " pdb=" O2C PIO B1001 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1A PIO A1001 " pdb=" O2C PIO A1001 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1A PIO D1001 " pdb=" O2C PIO D1001 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1A PIO C1001 " pdb=" O2C PIO C1001 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1B PIO D1001 " pdb=" O3C PIO D1001 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 26675 3.46 - 6.93: 441 6.93 - 10.39: 81 10.39 - 13.86: 24 13.86 - 17.32: 3 Bond angle restraints: 27224 Sorted by residual: angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 133.62 -17.32 3.50e+00 8.16e-02 2.45e+01 angle pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sigma weight residual 116.30 133.60 -17.30 3.50e+00 8.16e-02 2.44e+01 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 133.54 -17.24 3.50e+00 8.16e-02 2.43e+01 angle pdb=" C GLY A 626 " pdb=" N ASP A 627 " pdb=" CA ASP A 627 " ideal model delta sigma weight residual 122.07 128.79 -6.72 1.43e+00 4.89e-01 2.21e+01 angle pdb=" CA ASP A 627 " pdb=" CB ASP A 627 " pdb=" CG ASP A 627 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.00e+00 1.00e+00 1.71e+01 ... (remaining 27219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10682 17.85 - 35.70: 950 35.70 - 53.55: 164 53.55 - 71.40: 66 71.40 - 89.26: 18 Dihedral angle restraints: 11880 sinusoidal: 4800 harmonic: 7080 Sorted by residual: dihedral pdb=" CA TRP B 29 " pdb=" C TRP B 29 " pdb=" N GLU B 30 " pdb=" CA GLU B 30 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TRP A 29 " pdb=" C TRP A 29 " pdb=" N GLU A 30 " pdb=" CA GLU A 30 " ideal model delta harmonic sigma weight residual -180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TRP D 29 " pdb=" C TRP D 29 " pdb=" N GLU D 30 " pdb=" CA GLU D 30 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 11877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2929 0.119 - 0.237: 143 0.237 - 0.356: 20 0.356 - 0.475: 4 0.475 - 0.593: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CG LEU C 308 " pdb=" CB LEU C 308 " pdb=" CD1 LEU C 308 " pdb=" CD2 LEU C 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CG LEU A 308 " pdb=" CB LEU A 308 " pdb=" CD1 LEU A 308 " pdb=" CD2 LEU A 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CG LEU D 308 " pdb=" CB LEU D 308 " pdb=" CD1 LEU D 308 " pdb=" CD2 LEU D 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 3097 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 29 " 0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 29 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 29 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 29 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 29 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 29 " 0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A 29 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 29 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 29 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 29 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 29 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 29 " 0.023 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP D 29 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP D 29 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 29 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 29 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 29 " 0.002 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5573 2.82 - 3.34: 17961 3.34 - 3.86: 34043 3.86 - 4.38: 40047 4.38 - 4.90: 68049 Nonbonded interactions: 165673 Sorted by model distance: nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.300 3.040 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.300 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.300 3.040 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR D 379 " pdb=" OD2 ASP D 382 " model vdw 2.303 3.040 ... (remaining 165668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.310 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.007 0.093 20052 Z= 0.297 Angle : 1.158 17.321 27224 Z= 0.579 Chirality : 0.066 0.593 3100 Planarity : 0.008 0.073 3424 Dihedral : 14.764 89.255 7304 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.14), residues: 2408 helix: -1.95 (0.10), residues: 1436 sheet: 0.06 (0.49), residues: 92 loop : -1.35 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.034 0.003 TYR A 621 PHE 0.034 0.003 PHE B 456 TRP 0.055 0.003 TRP B 29 HIS 0.007 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.30 (20048) covalent geometry : angle 1.15778 / 0.58 (27224) hydrogen bonds : bond 0.13379 / 8.61 ( 1054) hydrogen bonds : angle 6.33429 / 4.55 ( 3090) Misc. bond : bond 0.00211 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.632 Fit side-chains REVERT: A 51 GLN cc_start: 0.8318 (tp40) cc_final: 0.8039 (mm-40) REVERT: A 260 MET cc_start: 0.8295 (mmm) cc_final: 0.7977 (mmm) REVERT: B 51 GLN cc_start: 0.8293 (tp40) cc_final: 0.8058 (mm-40) REVERT: B 260 MET cc_start: 0.8266 (mmm) cc_final: 0.7950 (mmm) REVERT: C 51 GLN cc_start: 0.8255 (tp40) cc_final: 0.8001 (mm-40) REVERT: C 260 MET cc_start: 0.8274 (mmm) cc_final: 0.7960 (mmm) REVERT: D 51 GLN cc_start: 0.8319 (tp40) cc_final: 0.8061 (mm-40) REVERT: D 260 MET cc_start: 0.8289 (mmm) cc_final: 0.7978 (mmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.5979 time to fit residues: 218.3682 Evaluate side-chains 225 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 306 GLN A 587 GLN B 129 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN C 129 ASN C 306 GLN D 267 GLN D 306 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119816 restraints weight = 22335.658| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.41 r_work: 0.3218 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20052 Z= 0.115 Angle : 0.559 5.474 27224 Z= 0.285 Chirality : 0.041 0.215 3100 Planarity : 0.005 0.056 3424 Dihedral : 6.293 57.415 2712 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.34 % Allowed : 8.40 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2408 helix: 0.23 (0.13), residues: 1404 sheet: 0.50 (0.48), residues: 84 loop : -0.88 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.014 0.001 TYR C 222 PHE 0.014 0.001 PHE C 537 TRP 0.023 0.001 TRP B 29 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (20048) covalent geometry : angle 0.55888 / 0.29 (27224) hydrogen bonds : bond 0.03976 / 2.70 ( 1054) hydrogen bonds : angle 4.03557 / 2.89 ( 3090) Misc. bond : bond 0.00111 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8718 (mmm) cc_final: 0.8299 (mmm) REVERT: A 466 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8778 (mtt) REVERT: B 35 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7250 (tpt90) REVERT: B 177 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6624 (tp30) REVERT: B 222 TYR cc_start: 0.7948 (m-80) cc_final: 0.7685 (m-80) REVERT: B 260 MET cc_start: 0.8716 (mmm) cc_final: 0.8304 (mmm) REVERT: B 309 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7314 (mt-10) REVERT: C 260 MET cc_start: 0.8711 (mmm) cc_final: 0.8233 (mmm) REVERT: D 35 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7207 (ttt90) REVERT: D 260 MET cc_start: 0.8721 (mmm) cc_final: 0.8307 (mmm) outliers start: 28 outliers final: 8 residues processed: 276 average time/residue: 0.5942 time to fit residues: 183.8307 Evaluate side-chains 220 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 78 optimal weight: 0.0670 chunk 120 optimal weight: 0.0870 chunk 192 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 221 optimal weight: 0.0070 chunk 157 optimal weight: 4.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN B 131 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN C 131 ASN C 267 GLN D 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119136 restraints weight = 22545.282| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.40 r_work: 0.3217 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20052 Z= 0.105 Angle : 0.512 5.184 27224 Z= 0.262 Chirality : 0.039 0.161 3100 Planarity : 0.004 0.055 3424 Dihedral : 5.800 59.616 2712 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.81 % Allowed : 12.17 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2408 helix: 0.97 (0.14), residues: 1428 sheet: 0.48 (0.47), residues: 84 loop : -0.54 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 33 TYR 0.017 0.001 TYR C 222 PHE 0.012 0.001 PHE C 537 TRP 0.020 0.001 TRP D 29 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (20048) covalent geometry : angle 0.51243 / 0.26 (27224) hydrogen bonds : bond 0.03554 / 2.42 ( 1054) hydrogen bonds : angle 3.70808 / 2.66 ( 3090) Misc. bond : bond 0.00016 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.7949 (mt0) cc_final: 0.7546 (mt0) REVERT: A 309 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 403 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: A 466 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8767 (mtt) REVERT: A 554 MET cc_start: 0.9132 (mmp) cc_final: 0.8759 (tpt) REVERT: A 596 GLN cc_start: 0.8401 (pt0) cc_final: 0.8135 (pt0) REVERT: B 35 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7269 (ttt90) REVERT: B 128 GLN cc_start: 0.7909 (mt0) cc_final: 0.7506 (mt0) REVERT: B 222 TYR cc_start: 0.7840 (m-80) cc_final: 0.7639 (m-80) REVERT: B 309 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 403 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: B 554 MET cc_start: 0.9147 (mmp) cc_final: 0.8793 (tpt) REVERT: B 596 GLN cc_start: 0.8397 (pt0) cc_final: 0.8126 (pt0) REVERT: C 42 GLU cc_start: 0.8069 (tt0) cc_final: 0.7845 (tt0) REVERT: C 128 GLN cc_start: 0.7906 (mt0) cc_final: 0.7501 (mt0) REVERT: C 403 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: C 554 MET cc_start: 0.9179 (mmp) cc_final: 0.8655 (tpt) REVERT: C 596 GLN cc_start: 0.8386 (pt0) cc_final: 0.8109 (pt0) REVERT: D 35 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7266 (ttt90) REVERT: D 42 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: D 128 GLN cc_start: 0.7964 (mt0) cc_final: 0.7531 (mt0) REVERT: D 309 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7452 (mt-10) REVERT: D 403 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: D 554 MET cc_start: 0.9178 (mmp) cc_final: 0.8680 (tpt) REVERT: D 596 GLN cc_start: 0.8397 (pt0) cc_final: 0.8131 (pt0) outliers start: 38 outliers final: 12 residues processed: 278 average time/residue: 0.6007 time to fit residues: 186.4026 Evaluate side-chains 240 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115804 restraints weight = 22566.982| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.34 r_work: 0.3140 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20052 Z= 0.143 Angle : 0.547 5.537 27224 Z= 0.279 Chirality : 0.041 0.166 3100 Planarity : 0.004 0.056 3424 Dihedral : 5.734 59.461 2712 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.39 % Allowed : 13.55 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2408 helix: 1.14 (0.14), residues: 1432 sheet: 0.49 (0.49), residues: 84 loop : -0.40 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.013 0.002 TYR C 222 PHE 0.011 0.001 PHE A 468 TRP 0.016 0.001 TRP A 29 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (20048) covalent geometry : angle 0.54725 / 0.28 (27224) hydrogen bonds : bond 0.03925 / 2.68 ( 1054) hydrogen bonds : angle 3.72454 / 2.68 ( 3090) Misc. bond : bond 0.00015 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.603 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: A 128 GLN cc_start: 0.8080 (mt0) cc_final: 0.7700 (mt0) REVERT: A 309 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 466 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8762 (mtt) REVERT: B 35 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7622 (ttt90) REVERT: B 128 GLN cc_start: 0.8040 (mt0) cc_final: 0.7670 (mt0) REVERT: B 309 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7893 (mt-10) REVERT: C 42 GLU cc_start: 0.8315 (tt0) cc_final: 0.8110 (tt0) REVERT: C 128 GLN cc_start: 0.8047 (mt0) cc_final: 0.7680 (mt0) REVERT: C 403 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: D 35 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7606 (ttt90) REVERT: D 128 GLN cc_start: 0.8059 (mt0) cc_final: 0.7667 (mt0) REVERT: D 309 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7887 (mt-10) outliers start: 50 outliers final: 22 residues processed: 248 average time/residue: 0.6173 time to fit residues: 170.0314 Evaluate side-chains 240 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 chunk 174 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 207 optimal weight: 0.0970 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115751 restraints weight = 22455.657| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.42 r_work: 0.3166 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20052 Z= 0.102 Angle : 0.501 5.115 27224 Z= 0.256 Chirality : 0.039 0.157 3100 Planarity : 0.004 0.053 3424 Dihedral : 5.450 56.784 2712 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.05 % Allowed : 14.41 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2408 helix: 1.43 (0.14), residues: 1432 sheet: -0.24 (0.50), residues: 92 loop : -0.17 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.014 0.001 TYR B 222 PHE 0.009 0.001 PHE C 537 TRP 0.011 0.001 TRP A 29 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (20048) covalent geometry : angle 0.50096 / 0.26 (27224) hydrogen bonds : bond 0.03449 / 2.35 ( 1054) hydrogen bonds : angle 3.60423 / 2.59 ( 3090) Misc. bond : bond 0.00006 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.661 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: A 128 GLN cc_start: 0.7759 (mt0) cc_final: 0.7355 (mt0) REVERT: A 303 GLU cc_start: 0.8568 (mp0) cc_final: 0.8361 (mp0) REVERT: A 309 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 466 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8724 (mtt) REVERT: A 554 MET cc_start: 0.9143 (mmp) cc_final: 0.8815 (tpt) REVERT: B 35 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7315 (ttt90) REVERT: B 128 GLN cc_start: 0.7708 (mt0) cc_final: 0.7304 (mt0) REVERT: B 309 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 554 MET cc_start: 0.9154 (mmp) cc_final: 0.8864 (tpt) REVERT: C 128 GLN cc_start: 0.7730 (mt0) cc_final: 0.7322 (mt0) REVERT: C 554 MET cc_start: 0.9124 (mmp) cc_final: 0.8819 (tpt) REVERT: D 35 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7311 (ttt90) REVERT: D 128 GLN cc_start: 0.7739 (mt0) cc_final: 0.7326 (mt0) REVERT: D 309 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 554 MET cc_start: 0.9173 (mmp) cc_final: 0.8849 (tpt) outliers start: 43 outliers final: 20 residues processed: 259 average time/residue: 0.6281 time to fit residues: 180.3049 Evaluate side-chains 239 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 267 GLN B 131 ASN C 31 GLN C 131 ASN D 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110259 restraints weight = 21590.925| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.58 r_work: 0.3135 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20052 Z= 0.207 Angle : 0.608 6.132 27224 Z= 0.311 Chirality : 0.044 0.180 3100 Planarity : 0.005 0.053 3424 Dihedral : 5.760 57.666 2712 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.34 % Allowed : 14.65 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2408 helix: 1.18 (0.14), residues: 1424 sheet: 0.35 (0.51), residues: 84 loop : -0.48 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 180 TYR 0.013 0.002 TYR C 222 PHE 0.013 0.002 PHE D 468 TRP 0.018 0.002 TRP D 29 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (20048) covalent geometry : angle 0.60786 / 0.31 (27224) hydrogen bonds : bond 0.04459 / 3.04 ( 1054) hydrogen bonds : angle 3.85226 / 2.77 ( 3090) Misc. bond : bond 0.00041 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: A 128 GLN cc_start: 0.7944 (mt0) cc_final: 0.7678 (mt0) REVERT: A 300 LYS cc_start: 0.8495 (mmpt) cc_final: 0.8181 (mmmt) REVERT: A 309 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8071 (mt-10) REVERT: A 403 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: A 466 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8941 (mtt) REVERT: B 35 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7376 (ttt90) REVERT: B 42 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: B 128 GLN cc_start: 0.7908 (mt0) cc_final: 0.7638 (mt0) REVERT: B 184 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7194 (mp0) REVERT: B 309 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 42 GLU cc_start: 0.8412 (tt0) cc_final: 0.8164 (tt0) REVERT: C 128 GLN cc_start: 0.7859 (mt0) cc_final: 0.7475 (mt0) REVERT: C 403 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: C 591 GLU cc_start: 0.7756 (mp0) cc_final: 0.7383 (tt0) REVERT: D 35 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7353 (ttt90) REVERT: D 42 GLU cc_start: 0.8441 (tt0) cc_final: 0.8220 (tt0) REVERT: D 128 GLN cc_start: 0.7940 (mt0) cc_final: 0.7656 (mt0) REVERT: D 309 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8072 (mt-10) REVERT: D 403 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: D 591 GLU cc_start: 0.7760 (mp0) cc_final: 0.7397 (tt0) outliers start: 49 outliers final: 18 residues processed: 253 average time/residue: 0.6240 time to fit residues: 175.1141 Evaluate side-chains 239 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 chunk 221 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN B 131 ASN C 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115748 restraints weight = 21562.783| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.58 r_work: 0.3212 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20052 Z= 0.106 Angle : 0.512 5.891 27224 Z= 0.265 Chirality : 0.039 0.185 3100 Planarity : 0.004 0.051 3424 Dihedral : 5.426 58.234 2712 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 15.79 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2408 helix: 1.46 (0.14), residues: 1428 sheet: -0.35 (0.51), residues: 92 loop : -0.14 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 180 TYR 0.013 0.001 TYR C 555 PHE 0.009 0.001 PHE C 537 TRP 0.011 0.001 TRP A 29 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (20048) covalent geometry : angle 0.51226 / 0.26 (27224) hydrogen bonds : bond 0.03493 / 2.38 ( 1054) hydrogen bonds : angle 3.64764 / 2.61 ( 3090) Misc. bond : bond 0.00054 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7565 (ttm-80) REVERT: A 128 GLN cc_start: 0.7626 (mt0) cc_final: 0.7235 (mt0) REVERT: A 303 GLU cc_start: 0.8725 (mp0) cc_final: 0.8447 (mp0) REVERT: A 309 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 554 MET cc_start: 0.9192 (mmp) cc_final: 0.8915 (tpt) REVERT: A 591 GLU cc_start: 0.7795 (mp0) cc_final: 0.7398 (tt0) REVERT: B 35 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7337 (ttt180) REVERT: B 128 GLN cc_start: 0.7579 (mt0) cc_final: 0.7186 (mt0) REVERT: B 184 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7097 (mp0) REVERT: B 309 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 403 GLU cc_start: 0.8355 (tt0) cc_final: 0.8152 (tt0) REVERT: B 554 MET cc_start: 0.9203 (mmp) cc_final: 0.8897 (tpt) REVERT: C 42 GLU cc_start: 0.8282 (tt0) cc_final: 0.8028 (tt0) REVERT: C 128 GLN cc_start: 0.7459 (mt0) cc_final: 0.7069 (mt0) REVERT: C 302 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7318 (ttt90) REVERT: C 554 MET cc_start: 0.9191 (mmp) cc_final: 0.8971 (tpt) REVERT: C 591 GLU cc_start: 0.7677 (mp0) cc_final: 0.7288 (tt0) REVERT: D 35 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7325 (ttt180) REVERT: D 128 GLN cc_start: 0.7600 (mt0) cc_final: 0.7179 (mt0) REVERT: D 302 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7419 (ttt90) REVERT: D 309 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7765 (mt-10) REVERT: D 591 GLU cc_start: 0.7708 (mp0) cc_final: 0.7308 (tt0) outliers start: 38 outliers final: 17 residues processed: 257 average time/residue: 0.6420 time to fit residues: 183.6401 Evaluate side-chains 241 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 131 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 239 optimal weight: 0.0060 chunk 121 optimal weight: 2.9990 chunk 217 optimal weight: 0.1980 chunk 179 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118531 restraints weight = 22469.519| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.41 r_work: 0.3069 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20052 Z= 0.102 Angle : 0.505 6.180 27224 Z= 0.261 Chirality : 0.039 0.226 3100 Planarity : 0.004 0.049 3424 Dihedral : 5.143 54.577 2712 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.43 % Allowed : 16.79 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2408 helix: 1.63 (0.14), residues: 1432 sheet: -0.46 (0.50), residues: 92 loop : -0.06 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 180 TYR 0.011 0.001 TYR B 222 PHE 0.010 0.001 PHE A 537 TRP 0.010 0.001 TRP D 29 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (20048) covalent geometry : angle 0.50533 / 0.26 (27224) hydrogen bonds : bond 0.03283 / 2.23 ( 1054) hydrogen bonds : angle 3.55101 / 2.54 ( 3090) Misc. bond : bond 0.00026 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7341 (ttm-80) REVERT: A 42 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 89 TYR cc_start: 0.8068 (m-80) cc_final: 0.7812 (m-80) REVERT: A 128 GLN cc_start: 0.7010 (mt0) cc_final: 0.6603 (mt0) REVERT: A 180 ARG cc_start: 0.6764 (mtt-85) cc_final: 0.6496 (mmt180) REVERT: A 302 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7143 (ttm110) REVERT: A 303 GLU cc_start: 0.8557 (mp0) cc_final: 0.8141 (mp0) REVERT: A 309 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 554 MET cc_start: 0.9128 (mmp) cc_final: 0.8727 (tpt) REVERT: A 591 GLU cc_start: 0.7283 (mp0) cc_final: 0.6932 (tt0) REVERT: A 596 GLN cc_start: 0.8276 (pt0) cc_final: 0.8034 (pt0) REVERT: B 35 ARG cc_start: 0.7386 (ttm110) cc_final: 0.7008 (ttt180) REVERT: B 89 TYR cc_start: 0.8056 (m-80) cc_final: 0.7770 (m-80) REVERT: B 128 GLN cc_start: 0.6947 (mt0) cc_final: 0.6530 (mt0) REVERT: B 180 ARG cc_start: 0.6833 (mtt-85) cc_final: 0.6376 (mmt180) REVERT: B 309 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 554 MET cc_start: 0.9136 (mmp) cc_final: 0.8744 (tpt) REVERT: B 596 GLN cc_start: 0.8253 (pt0) cc_final: 0.8003 (pt0) REVERT: C 42 GLU cc_start: 0.8105 (tt0) cc_final: 0.7847 (tt0) REVERT: C 128 GLN cc_start: 0.7190 (mt0) cc_final: 0.6763 (mt0) REVERT: C 309 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 596 GLN cc_start: 0.8275 (pt0) cc_final: 0.8034 (pt0) REVERT: D 35 ARG cc_start: 0.7378 (ttm110) cc_final: 0.7024 (ttt180) REVERT: D 89 TYR cc_start: 0.8042 (m-80) cc_final: 0.7779 (m-80) REVERT: D 128 GLN cc_start: 0.7084 (mt0) cc_final: 0.6670 (mt0) REVERT: D 309 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7484 (mt-10) REVERT: D 596 GLN cc_start: 0.8284 (pt0) cc_final: 0.8028 (pt0) outliers start: 30 outliers final: 16 residues processed: 256 average time/residue: 0.6340 time to fit residues: 180.8183 Evaluate side-chains 243 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 234 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111727 restraints weight = 21420.775| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.58 r_work: 0.3154 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20052 Z= 0.174 Angle : 0.588 7.293 27224 Z= 0.300 Chirality : 0.043 0.271 3100 Planarity : 0.004 0.049 3424 Dihedral : 5.349 59.667 2712 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.53 % Allowed : 17.22 % Favored : 81.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2408 helix: 1.40 (0.14), residues: 1424 sheet: -0.44 (0.51), residues: 92 loop : -0.20 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 180 TYR 0.013 0.002 TYR C 222 PHE 0.012 0.001 PHE A 468 TRP 0.017 0.001 TRP B 29 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (20048) covalent geometry : angle 0.58759 / 0.30 (27224) hydrogen bonds : bond 0.04136 / 2.81 ( 1054) hydrogen bonds : angle 3.73492 / 2.67 ( 3090) Misc. bond : bond 0.00060 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7639 (ttm-80) REVERT: A 42 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 128 GLN cc_start: 0.7626 (mt0) cc_final: 0.7336 (mt0) REVERT: A 184 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 300 LYS cc_start: 0.8445 (mmpt) cc_final: 0.8118 (mmmt) REVERT: A 302 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7541 (ttm110) REVERT: A 303 GLU cc_start: 0.8723 (mp0) cc_final: 0.8510 (mp0) REVERT: A 309 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8020 (mt-10) REVERT: A 554 MET cc_start: 0.9190 (mmp) cc_final: 0.8850 (tpt) REVERT: A 591 GLU cc_start: 0.7726 (mp0) cc_final: 0.7385 (tt0) REVERT: B 35 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7336 (ttt180) REVERT: B 42 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: B 128 GLN cc_start: 0.7522 (mt0) cc_final: 0.7141 (mt0) REVERT: B 180 ARG cc_start: 0.6913 (mtt-85) cc_final: 0.6637 (mmt180) REVERT: B 309 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 403 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: B 554 MET cc_start: 0.9199 (mmp) cc_final: 0.8872 (tpt) REVERT: C 42 GLU cc_start: 0.8413 (tt0) cc_final: 0.8166 (tt0) REVERT: C 128 GLN cc_start: 0.7654 (mt0) cc_final: 0.7360 (mt0) REVERT: C 300 LYS cc_start: 0.8455 (mmpt) cc_final: 0.8113 (mmmt) REVERT: C 309 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7966 (mt-10) REVERT: C 403 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: C 591 GLU cc_start: 0.7689 (mp0) cc_final: 0.7339 (tt0) REVERT: D 35 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7335 (ttt180) REVERT: D 128 GLN cc_start: 0.7529 (mt0) cc_final: 0.7130 (mt0) REVERT: D 300 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8120 (mmmt) REVERT: D 309 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 591 GLU cc_start: 0.7709 (mp0) cc_final: 0.7325 (tt0) outliers start: 32 outliers final: 21 residues processed: 246 average time/residue: 0.6822 time to fit residues: 186.8376 Evaluate side-chains 246 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113848 restraints weight = 21529.020| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.58 r_work: 0.3198 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20052 Z= 0.132 Angle : 0.552 7.508 27224 Z= 0.285 Chirality : 0.041 0.273 3100 Planarity : 0.004 0.049 3424 Dihedral : 5.221 58.379 2712 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.29 % Allowed : 17.32 % Favored : 81.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2408 helix: 1.41 (0.14), residues: 1428 sheet: -0.47 (0.50), residues: 92 loop : -0.10 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.011 0.001 TYR B 222 PHE 0.008 0.001 PHE A 468 TRP 0.013 0.001 TRP A 29 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (20048) covalent geometry : angle 0.55190 / 0.28 (27224) hydrogen bonds : bond 0.03732 / 2.55 ( 1054) hydrogen bonds : angle 3.69175 / 2.64 ( 3090) Misc. bond : bond 0.00103 / 0.05 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.647 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: A 35 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7671 (ttm-80) REVERT: A 42 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 107 LYS cc_start: 0.7661 (mptt) cc_final: 0.7223 (mptt) REVERT: A 128 GLN cc_start: 0.7428 (mt0) cc_final: 0.7027 (mt0) REVERT: A 184 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7317 (mp0) REVERT: A 300 LYS cc_start: 0.8374 (mmpt) cc_final: 0.8045 (mmmt) REVERT: A 309 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 554 MET cc_start: 0.9194 (mmp) cc_final: 0.8934 (tpt) REVERT: A 591 GLU cc_start: 0.7725 (mp0) cc_final: 0.7346 (tt0) REVERT: B 35 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7343 (ttt180) REVERT: B 42 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: B 128 GLN cc_start: 0.7443 (mt0) cc_final: 0.7058 (mt0) REVERT: B 180 ARG cc_start: 0.6909 (mtt-85) cc_final: 0.6663 (mmt180) REVERT: B 309 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 554 MET cc_start: 0.9195 (mmp) cc_final: 0.8931 (tpt) REVERT: C 42 GLU cc_start: 0.8349 (tt0) cc_final: 0.8119 (tt0) REVERT: C 128 GLN cc_start: 0.7479 (mt0) cc_final: 0.7091 (mt0) REVERT: C 129 ASN cc_start: 0.8368 (p0) cc_final: 0.8082 (t0) REVERT: C 300 LYS cc_start: 0.8371 (mmpt) cc_final: 0.8063 (mmmt) REVERT: C 309 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 554 MET cc_start: 0.9225 (mmp) cc_final: 0.8899 (tpt) REVERT: C 591 GLU cc_start: 0.7695 (mp0) cc_final: 0.7303 (tt0) REVERT: D 35 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7342 (ttt180) REVERT: D 128 GLN cc_start: 0.7504 (mt0) cc_final: 0.7094 (mt0) REVERT: D 300 LYS cc_start: 0.8376 (mmpt) cc_final: 0.8082 (mmmt) REVERT: D 309 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7815 (mt-10) REVERT: D 554 MET cc_start: 0.9204 (mmp) cc_final: 0.8905 (tpt) REVERT: D 591 GLU cc_start: 0.7693 (mp0) cc_final: 0.7288 (tt0) outliers start: 27 outliers final: 17 residues processed: 247 average time/residue: 0.7066 time to fit residues: 193.7959 Evaluate side-chains 245 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113670 restraints weight = 22446.862| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.40 r_work: 0.3142 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20052 Z= 0.135 Angle : 0.553 7.321 27224 Z= 0.284 Chirality : 0.041 0.276 3100 Planarity : 0.004 0.049 3424 Dihedral : 5.153 53.702 2712 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.19 % Allowed : 17.46 % Favored : 81.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2408 helix: 1.40 (0.14), residues: 1428 sheet: -0.51 (0.50), residues: 92 loop : -0.13 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.011 0.001 TYR B 222 PHE 0.009 0.001 PHE A 468 TRP 0.014 0.001 TRP A 29 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (20048) covalent geometry : angle 0.55293 / 0.28 (27224) hydrogen bonds : bond 0.03816 / 2.60 ( 1054) hydrogen bonds : angle 3.68830 / 2.64 ( 3090) Misc. bond : bond 0.00136 / 0.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6034.87 seconds wall clock time: 103 minutes 39.22 seconds (6219.22 seconds total)