Starting phenix.real_space_refine on Sat Mar 7 03:11:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sih_10210/03_2026/6sih_10210.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sih_10210/03_2026/6sih_10210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sih_10210/03_2026/6sih_10210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sih_10210/03_2026/6sih_10210.map" model { file = "/net/cci-nas-00/data/ceres_data/6sih_10210/03_2026/6sih_10210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sih_10210/03_2026/6sih_10210.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 23150 2.51 5 N 6140 2.21 5 O 7910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Restraints were copied for chains: H, B, F, C, G, D, I, E, J Time building chain proxies: 4.55, per 1000 atoms: 0.12 Number of scatterers: 37310 At special positions: 0 Unit cell: (138, 144.9, 296.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 7910 8.00 N 6140 7.00 C 23150 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=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 9640 Ramachandran restraints generated. 4820 Oldfield, 0 Emsley, 4820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9080 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 51 sheets defined 46.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 17 through 67 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 638 removed outlier: 3.546A pdb=" N ILE A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 590 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 606 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 67 Proline residue: H 35 - end of helix Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 154 through 166 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS H 306 " --> pdb=" O GLU H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 357 removed outlier: 4.364A pdb=" N ASN H 345 " --> pdb=" O ILE H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 384 Processing helix chain 'H' and resid 397 through 408 Processing helix chain 'H' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR H 412 " --> pdb=" O ASP H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS H 563 " --> pdb=" O GLY H 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU H 564 " --> pdb=" O ILE H 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE H 589 " --> pdb=" O LEU H 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 590 " --> pdb=" O THR H 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 606 " --> pdb=" O MET H 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR H 607 " --> pdb=" O ILE H 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR H 609 " --> pdb=" O THR H 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 67 Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 154 through 166 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 638 removed outlier: 3.546A pdb=" N ILE B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 606 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 67 Proline residue: F 35 - end of helix Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 154 through 166 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 218 through 225 Processing helix chain 'F' and resid 302 through 326 removed outlier: 4.148A pdb=" N LYS F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 357 removed outlier: 4.362A pdb=" N ASN F 345 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 384 Processing helix chain 'F' and resid 397 through 408 Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS F 563 " --> pdb=" O GLY F 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 564 " --> pdb=" O ILE F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE F 589 " --> pdb=" O LEU F 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 590 " --> pdb=" O THR F 586 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG F 606 " --> pdb=" O MET F 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR F 607 " --> pdb=" O ILE F 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 609 " --> pdb=" O THR F 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 67 Proline residue: C 35 - end of helix Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 154 through 166 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 357 removed outlier: 4.364A pdb=" N ASN C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 397 through 408 Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 590 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 606 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 607 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 609 " --> pdb=" O THR C 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 67 Proline residue: G 35 - end of helix Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 154 through 166 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 218 through 225 Processing helix chain 'G' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS G 306 " --> pdb=" O GLU G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 357 removed outlier: 4.364A pdb=" N ASN G 345 " --> pdb=" O ILE G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 384 Processing helix chain 'G' and resid 397 through 408 Processing helix chain 'G' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR G 412 " --> pdb=" O ASP G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS G 563 " --> pdb=" O GLY G 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 564 " --> pdb=" O ILE G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 576 through 638 removed outlier: 3.546A pdb=" N ILE G 589 " --> pdb=" O LEU G 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 590 " --> pdb=" O THR G 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG G 606 " --> pdb=" O MET G 602 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 607 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 609 " --> pdb=" O THR G 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 67 Proline residue: D 35 - end of helix Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 154 through 166 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 397 through 408 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS D 563 " --> pdb=" O GLY D 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 564 " --> pdb=" O ILE D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 638 removed outlier: 3.548A pdb=" N ILE D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 590 " --> pdb=" O THR D 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 606 " --> pdb=" O MET D 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR D 607 " --> pdb=" O ILE D 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 609 " --> pdb=" O THR D 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 67 Proline residue: I 35 - end of helix Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'I' and resid 154 through 166 Processing helix chain 'I' and resid 194 through 197 Processing helix chain 'I' and resid 218 through 225 Processing helix chain 'I' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS I 306 " --> pdb=" O GLU I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 357 removed outlier: 4.362A pdb=" N ASN I 345 " --> pdb=" O ILE I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 384 Processing helix chain 'I' and resid 397 through 408 Processing helix chain 'I' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR I 412 " --> pdb=" O ASP I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS I 563 " --> pdb=" O GLY I 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 564 " --> pdb=" O ILE I 560 " (cutoff:3.500A) Processing helix chain 'I' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE I 589 " --> pdb=" O LEU I 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 590 " --> pdb=" O THR I 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG I 606 " --> pdb=" O MET I 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR I 607 " --> pdb=" O ILE I 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR I 609 " --> pdb=" O THR I 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 67 Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 154 through 166 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 302 through 326 removed outlier: 4.148A pdb=" N LYS E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 384 Processing helix chain 'E' and resid 397 through 408 Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS E 563 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 564 " --> pdb=" O ILE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE E 589 " --> pdb=" O LEU E 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 590 " --> pdb=" O THR E 586 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG E 606 " --> pdb=" O MET E 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 607 " --> pdb=" O ILE E 603 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 609 " --> pdb=" O THR E 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 67 Proline residue: J 35 - end of helix Processing helix chain 'J' and resid 69 through 73 Processing helix chain 'J' and resid 154 through 166 Processing helix chain 'J' and resid 194 through 197 Processing helix chain 'J' and resid 218 through 225 Processing helix chain 'J' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS J 306 " --> pdb=" O GLU J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 341 through 357 removed outlier: 4.362A pdb=" N ASN J 345 " --> pdb=" O ILE J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 384 Processing helix chain 'J' and resid 397 through 408 Processing helix chain 'J' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR J 412 " --> pdb=" O ASP J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS J 563 " --> pdb=" O GLY J 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU J 564 " --> pdb=" O ILE J 560 " (cutoff:3.500A) Processing helix chain 'J' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE J 589 " --> pdb=" O LEU J 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS J 590 " --> pdb=" O THR J 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG J 606 " --> pdb=" O MET J 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR J 607 " --> pdb=" O ILE J 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR J 609 " --> pdb=" O THR J 605 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN A 99 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL A 105 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 263 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 107 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET A 283 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP A 278 " --> pdb=" O MET A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG A 185 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 149 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA6, first strand: chain 'H' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN H 99 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL H 105 " --> pdb=" O THR H 263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR H 263 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 107 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET H 283 " --> pdb=" O ASP H 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP H 278 " --> pdb=" O MET H 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG H 185 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 143 through 149 Processing sheet with id=AB1, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN B 99 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL B 105 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 263 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 107 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET B 283 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 278 " --> pdb=" O MET B 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG B 185 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 143 through 149 Processing sheet with id=AB6, first strand: chain 'B' and resid 386 through 387 Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN F 99 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL F 105 " --> pdb=" O THR F 263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR F 263 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 107 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET F 283 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP F 278 " --> pdb=" O MET F 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG F 185 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 143 through 149 Processing sheet with id=AC2, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AC3, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.715A pdb=" N LEU C 9 " --> pdb=" O LEU G 9 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 9 " --> pdb=" O LEU C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN C 99 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL C 105 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 263 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN C 107 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET C 283 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP C 278 " --> pdb=" O MET C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG C 185 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 143 through 149 Processing sheet with id=AC8, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC9, first strand: chain 'G' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN G 99 " --> pdb=" O VAL G 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL G 105 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR G 263 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN G 107 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET G 283 " --> pdb=" O ASP G 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP G 278 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG G 185 " --> pdb=" O VAL G 175 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 143 through 149 Processing sheet with id=AD4, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AD5, first strand: chain 'D' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN D 99 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL D 105 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 263 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN D 107 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET D 283 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP D 278 " --> pdb=" O MET D 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG D 185 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 143 through 149 Processing sheet with id=AD9, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AE1, first strand: chain 'I' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN I 99 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL I 105 " --> pdb=" O THR I 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR I 263 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I 107 " --> pdb=" O GLU I 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET I 283 " --> pdb=" O ASP I 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP I 278 " --> pdb=" O MET I 283 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG I 185 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 143 through 149 Processing sheet with id=AE5, first strand: chain 'I' and resid 386 through 387 Processing sheet with id=AE6, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN E 99 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL E 105 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 263 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN E 107 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET E 283 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP E 278 " --> pdb=" O MET E 283 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG E 185 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 143 through 149 Processing sheet with id=AF1, first strand: chain 'E' and resid 386 through 387 Processing sheet with id=AF2, first strand: chain 'J' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN J 99 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL J 105 " --> pdb=" O THR J 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR J 263 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN J 107 " --> pdb=" O GLU J 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET J 283 " --> pdb=" O ASP J 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP J 278 " --> pdb=" O MET J 283 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG J 185 " --> pdb=" O VAL J 175 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 143 through 149 Processing sheet with id=AF6, first strand: chain 'J' and resid 386 through 387 2160 hydrogen bonds defined for protein. 6150 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: 8.00 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12480 1.34 - 1.46: 6947 1.46 - 1.57: 18083 1.57 - 1.69: 0 1.69 - 1.80: 220 Bond restraints: 37730 Sorted by residual: bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.42e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.41e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.41e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.38e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.38e+00 ... (remaining 37725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 48477 1.10 - 2.20: 2111 2.20 - 3.30: 262 3.30 - 4.40: 80 4.40 - 5.51: 10 Bond angle restraints: 50940 Sorted by residual: angle pdb=" N ASP H 249 " pdb=" CA ASP H 249 " pdb=" C ASP H 249 " ideal model delta sigma weight residual 110.80 116.31 -5.51 2.13e+00 2.20e-01 6.68e+00 angle pdb=" N ASP A 249 " pdb=" CA ASP A 249 " pdb=" C ASP A 249 " ideal model delta sigma weight residual 110.80 116.29 -5.49 2.13e+00 2.20e-01 6.63e+00 angle pdb=" N ASP E 249 " pdb=" CA ASP E 249 " pdb=" C ASP E 249 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 angle pdb=" N ASP D 249 " pdb=" CA ASP D 249 " pdb=" C ASP D 249 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 angle pdb=" N ASP G 249 " pdb=" CA ASP G 249 " pdb=" C ASP G 249 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 ... (remaining 50935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 21214 16.81 - 33.62: 1396 33.62 - 50.43: 220 50.43 - 67.23: 80 67.23 - 84.04: 50 Dihedral angle restraints: 22960 sinusoidal: 8900 harmonic: 14060 Sorted by residual: dihedral pdb=" CA LYS B 248 " pdb=" C LYS B 248 " pdb=" N ASP B 249 " pdb=" CA ASP B 249 " ideal model delta harmonic sigma weight residual 180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS F 248 " pdb=" C LYS F 248 " pdb=" N ASP F 249 " pdb=" CA ASP F 249 " ideal model delta harmonic sigma weight residual 180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LYS A 248 " pdb=" C LYS A 248 " pdb=" N ASP A 249 " pdb=" CA ASP A 249 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 22957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3726 0.024 - 0.049: 1502 0.049 - 0.073: 393 0.073 - 0.098: 267 0.098 - 0.122: 122 Chirality restraints: 6010 Sorted by residual: chirality pdb=" CA ILE E 236 " pdb=" N ILE E 236 " pdb=" C ILE E 236 " pdb=" CB ILE E 236 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE B 236 " pdb=" N ILE B 236 " pdb=" C ILE B 236 " pdb=" CB ILE B 236 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ILE C 236 " pdb=" N ILE C 236 " pdb=" C ILE C 236 " pdb=" CB ILE C 236 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 6007 not shown) Planarity restraints: 6610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 248 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS F 248 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS F 248 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP F 249 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 248 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS J 248 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS J 248 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP J 249 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 248 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS I 248 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS I 248 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP I 249 " -0.008 2.00e-02 2.50e+03 ... (remaining 6607 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 601 2.52 - 3.12: 32758 3.12 - 3.71: 60122 3.71 - 4.31: 84182 4.31 - 4.90: 135944 Nonbonded interactions: 313607 Sorted by model distance: nonbonded pdb=" O GLY A 14 " pdb=" OG SER B 7 " model vdw 1.931 3.040 nonbonded pdb=" O GLY B 14 " pdb=" OG SER C 7 " model vdw 1.960 3.040 nonbonded pdb=" O GLY H 14 " pdb=" OG SER I 7 " model vdw 1.978 3.040 nonbonded pdb=" OG SER F 7 " pdb=" O GLY G 14 " model vdw 1.982 3.040 nonbonded pdb=" OG SER H 7 " pdb=" O GLY F 14 " model vdw 1.987 3.040 ... (remaining 313602 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'B' selection = chain 'F' selection = chain 'C' selection = chain 'G' selection = chain 'D' selection = chain 'I' selection = chain 'E' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'B' selection = chain 'F' selection = chain 'C' selection = chain 'G' selection = chain 'D' selection = chain 'I' selection = chain 'E' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.200 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 37730 Z= 0.245 Angle : 0.544 5.506 50940 Z= 0.327 Chirality : 0.035 0.122 6010 Planarity : 0.002 0.013 6610 Dihedral : 12.608 84.043 13880 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.62 (0.11), residues: 4820 helix: -0.40 (0.10), residues: 2090 sheet: -0.96 (0.16), residues: 770 loop : -1.77 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 271 TYR 0.005 0.001 TYR E 607 PHE 0.012 0.001 PHE E 139 TRP 0.007 0.002 TRP F 614 HIS 0.002 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00456 (37730) covalent geometry : angle 0.54402 (50940) hydrogen bonds : bond 0.15441 ( 2160) hydrogen bonds : angle 7.08063 ( 6150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9640 Ramachandran restraints generated. 4820 Oldfield, 0 Emsley, 4820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9640 Ramachandran restraints generated. 4820 Oldfield, 0 Emsley, 4820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 201 PHE cc_start: 0.6738 (m-80) cc_final: 0.5743 (m-80) REVERT: A 212 TYR cc_start: 0.7966 (m-10) cc_final: 0.7321 (t80) REVERT: A 610 MET cc_start: 0.8621 (mmm) cc_final: 0.8301 (mmm) REVERT: A 624 LEU cc_start: 0.8830 (tt) cc_final: 0.8583 (mm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1015 time to fit residues: 4.0433 Evaluate side-chains 21 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 0.3980 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN H 107 GLN H 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.038211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.029911 restraints weight = 50341.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.030769 restraints weight = 31409.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.031338 restraints weight = 22925.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.031722 restraints weight = 18608.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.031980 restraints weight = 16143.344| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37730 Z= 0.141 Angle : 0.633 10.338 50940 Z= 0.328 Chirality : 0.042 0.162 6010 Planarity : 0.004 0.059 6610 Dihedral : 5.256 29.495 5050 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -0.18 (0.12), residues: 4820 helix: 1.37 (0.11), residues: 2040 sheet: -0.54 (0.16), residues: 810 loop : -1.54 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 606 TYR 0.024 0.002 TYR H 617 PHE 0.010 0.002 PHE H 384 TRP 0.008 0.001 TRP J 227 HIS 0.002 0.002 HIS G 253 Details of bonding type rmsd covalent geometry : bond 0.00265 (37730) covalent geometry : angle 0.63285 (50940) hydrogen bonds : bond 0.04693 ( 2160) hydrogen bonds : angle 5.44031 ( 6150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: H 262 PHE cc_start: 0.7936 (m-80) cc_final: 0.7658 (m-80) REVERT: H 269 MET cc_start: 0.8094 (mmp) cc_final: 0.7509 (mmm) REVERT: H 570 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8988 (pt0) REVERT: H 603 ILE cc_start: 0.8687 (mt) cc_final: 0.8441 (mt) REVERT: H 617 TYR cc_start: 0.7042 (p90) cc_final: 0.6177 (m-10) REVERT: H 624 LEU cc_start: 0.9037 (tt) cc_final: 0.8646 (mm) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0674 time to fit residues: 2.4929 Evaluate side-chains 19 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 442 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 434 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 chunk 415 optimal weight: 9.9990 chunk 420 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 90 optimal weight: 0.0030 chunk 34 optimal weight: 0.6980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.037970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029743 restraints weight = 50874.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.030574 restraints weight = 32000.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.031133 restraints weight = 23586.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.031511 restraints weight = 19209.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.031642 restraints weight = 16688.849| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 37730 Z= 0.117 Angle : 0.572 8.296 50940 Z= 0.300 Chirality : 0.041 0.195 6010 Planarity : 0.003 0.046 6610 Dihedral : 5.187 28.824 5050 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: 0.09 (0.12), residues: 4820 helix: 1.59 (0.11), residues: 2040 sheet: -0.43 (0.16), residues: 810 loop : -1.38 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 348 TYR 0.010 0.001 TYR B 202 PHE 0.012 0.001 PHE H 139 TRP 0.008 0.002 TRP A 227 HIS 0.001 0.001 HIS G 253 Details of bonding type rmsd covalent geometry : bond 0.00230 (37730) covalent geometry : angle 0.57177 (50940) hydrogen bonds : bond 0.04281 ( 2160) hydrogen bonds : angle 5.24628 ( 6150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: H 269 MET cc_start: 0.8125 (mmp) cc_final: 0.7575 (mmm) REVERT: H 283 MET cc_start: 0.7961 (ptp) cc_final: 0.7760 (ptp) REVERT: H 571 MET cc_start: 0.8802 (mmp) cc_final: 0.8522 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0573 time to fit residues: 1.7670 Evaluate side-chains 16 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 166 optimal weight: 5.9990 chunk 76 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 403 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 389 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.038162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.030051 restraints weight = 51335.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.030921 restraints weight = 32448.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.031487 restraints weight = 23802.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.031861 restraints weight = 19288.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032118 restraints weight = 16805.358| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37730 Z= 0.131 Angle : 0.595 8.416 50940 Z= 0.308 Chirality : 0.041 0.188 6010 Planarity : 0.003 0.020 6610 Dihedral : 5.102 27.831 5050 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 0.34 (0.12), residues: 4820 helix: 1.89 (0.11), residues: 2040 sheet: -0.31 (0.17), residues: 810 loop : -1.35 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 606 TYR 0.011 0.001 TYR A 617 PHE 0.011 0.001 PHE A 139 TRP 0.017 0.003 TRP B 614 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00269 (37730) covalent geometry : angle 0.59532 (50940) hydrogen bonds : bond 0.04069 ( 2160) hydrogen bonds : angle 5.00764 ( 6150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: H 201 PHE cc_start: 0.7232 (m-80) cc_final: 0.6433 (m-80) REVERT: H 269 MET cc_start: 0.8029 (mmp) cc_final: 0.7791 (mmm) REVERT: H 283 MET cc_start: 0.8239 (ptp) cc_final: 0.7929 (ptp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0855 time to fit residues: 2.4118 Evaluate side-chains 16 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 337 optimal weight: 6.9990 chunk 376 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 397 optimal weight: 0.8980 chunk 335 optimal weight: 6.9990 chunk 406 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 462 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 438 optimal weight: 0.7980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.037465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.029087 restraints weight = 50727.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.029888 restraints weight = 32974.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.030418 restraints weight = 24524.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.030768 restraints weight = 20072.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.031002 restraints weight = 17596.853| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37730 Z= 0.156 Angle : 0.586 7.535 50940 Z= 0.307 Chirality : 0.041 0.201 6010 Planarity : 0.004 0.062 6610 Dihedral : 5.271 31.546 5050 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.40 (0.13), residues: 4820 helix: 2.01 (0.11), residues: 2040 sheet: -0.20 (0.17), residues: 810 loop : -1.46 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 348 TYR 0.013 0.002 TYR J 202 PHE 0.015 0.002 PHE B 139 TRP 0.007 0.002 TRP A 227 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (37730) covalent geometry : angle 0.58596 (50940) hydrogen bonds : bond 0.03843 ( 2160) hydrogen bonds : angle 5.13873 ( 6150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: H 201 PHE cc_start: 0.7311 (m-80) cc_final: 0.6577 (m-80) REVERT: H 262 PHE cc_start: 0.8000 (m-80) cc_final: 0.7787 (m-80) REVERT: H 269 MET cc_start: 0.8035 (mmp) cc_final: 0.7788 (mmm) REVERT: H 378 MET cc_start: 0.5602 (ttt) cc_final: 0.4841 (ttt) REVERT: H 615 LEU cc_start: 0.9516 (pp) cc_final: 0.9249 (tp) REVERT: H 634 MET cc_start: 0.6879 (pmm) cc_final: 0.6526 (pmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0595 time to fit residues: 1.5236 Evaluate side-chains 16 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 135 optimal weight: 7.9990 chunk 467 optimal weight: 10.0000 chunk 413 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 434 optimal weight: 4.9990 chunk 216 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 372 optimal weight: 0.0970 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.038546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030428 restraints weight = 50956.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.031233 restraints weight = 32649.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.031803 restraints weight = 24243.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032163 restraints weight = 19702.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.032412 restraints weight = 17191.439| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37730 Z= 0.140 Angle : 0.572 7.295 50940 Z= 0.297 Chirality : 0.040 0.166 6010 Planarity : 0.003 0.033 6610 Dihedral : 5.285 27.766 5050 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: 0.57 (0.13), residues: 4820 helix: 2.31 (0.11), residues: 2040 sheet: -0.06 (0.17), residues: 790 loop : -1.58 (0.15), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 606 TYR 0.010 0.001 TYR E 202 PHE 0.014 0.002 PHE I 139 TRP 0.005 0.001 TRP A 227 HIS 0.000 0.000 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00275 (37730) covalent geometry : angle 0.57231 (50940) hydrogen bonds : bond 0.03667 ( 2160) hydrogen bonds : angle 4.93847 ( 6150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: D 201 PHE cc_start: 0.7334 (m-80) cc_final: 0.6765 (m-10) REVERT: D 634 MET cc_start: 0.6477 (pmm) cc_final: 0.6209 (pmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0515 time to fit residues: 1.4896 Evaluate side-chains 16 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 15 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 289 optimal weight: 0.3980 chunk 297 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 445 optimal weight: 0.0010 chunk 394 optimal weight: 0.9980 chunk 417 optimal weight: 0.0020 chunk 143 optimal weight: 5.9990 chunk 204 optimal weight: 0.3980 chunk 186 optimal weight: 0.0870 overall best weight: 0.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.039491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031266 restraints weight = 50278.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.032124 restraints weight = 32223.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.032706 restraints weight = 23870.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.033109 restraints weight = 19375.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.033378 restraints weight = 16698.828| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37730 Z= 0.116 Angle : 0.605 10.970 50940 Z= 0.309 Chirality : 0.041 0.153 6010 Planarity : 0.002 0.024 6610 Dihedral : 5.070 24.502 5050 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 0.58 (0.13), residues: 4820 helix: 2.45 (0.11), residues: 2040 sheet: -0.18 (0.17), residues: 790 loop : -1.67 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 606 TYR 0.010 0.001 TYR J 607 PHE 0.013 0.002 PHE I 3 TRP 0.010 0.001 TRP A 227 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00235 (37730) covalent geometry : angle 0.60490 (50940) hydrogen bonds : bond 0.03518 ( 2160) hydrogen bonds : angle 4.67415 ( 6150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: D 201 PHE cc_start: 0.7294 (m-80) cc_final: 0.6518 (m-80) REVERT: D 269 MET cc_start: 0.7749 (mmp) cc_final: 0.7168 (mmm) REVERT: D 615 LEU cc_start: 0.9413 (pp) cc_final: 0.9193 (tp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0724 time to fit residues: 2.1277 Evaluate side-chains 16 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 42 optimal weight: 0.0040 chunk 166 optimal weight: 1.9990 chunk 463 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 359 optimal weight: 0.0040 chunk 387 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 360 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.039532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.031229 restraints weight = 50741.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032073 restraints weight = 33299.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.032656 restraints weight = 24826.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.033039 restraints weight = 20198.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.033323 restraints weight = 17523.829| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37730 Z= 0.103 Angle : 0.570 7.797 50940 Z= 0.289 Chirality : 0.040 0.148 6010 Planarity : 0.005 0.110 6610 Dihedral : 4.827 23.126 5050 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.57 (0.12), residues: 4820 helix: 2.24 (0.11), residues: 2110 sheet: -0.16 (0.17), residues: 790 loop : -1.60 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 606 TYR 0.010 0.001 TYR H 607 PHE 0.010 0.001 PHE J 139 TRP 0.009 0.001 TRP A 227 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00210 (37730) covalent geometry : angle 0.57017 (50940) hydrogen bonds : bond 0.03308 ( 2160) hydrogen bonds : angle 4.28604 ( 6150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: D 201 PHE cc_start: 0.7134 (m-80) cc_final: 0.6430 (m-80) REVERT: D 269 MET cc_start: 0.7760 (mmp) cc_final: 0.7272 (mmm) REVERT: D 615 LEU cc_start: 0.9395 (pp) cc_final: 0.9173 (tp) REVERT: D 628 LEU cc_start: 0.8709 (mm) cc_final: 0.8413 (pp) REVERT: D 634 MET cc_start: 0.6167 (tmm) cc_final: 0.5596 (ppp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0480 time to fit residues: 1.4740 Evaluate side-chains 18 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 388 optimal weight: 6.9990 chunk 436 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 404 optimal weight: 0.0770 chunk 446 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 154 optimal weight: 0.0010 chunk 418 optimal weight: 8.9990 chunk 86 optimal weight: 0.0670 chunk 255 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 overall best weight: 1.6286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030768 restraints weight = 50013.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031597 restraints weight = 32633.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032152 restraints weight = 24318.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.032546 restraints weight = 19827.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.032810 restraints weight = 17227.723| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37730 Z= 0.111 Angle : 0.559 7.306 50940 Z= 0.285 Chirality : 0.039 0.142 6010 Planarity : 0.004 0.087 6610 Dihedral : 4.725 22.742 5050 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.66 (0.13), residues: 4820 helix: 2.36 (0.11), residues: 2110 sheet: -0.19 (0.17), residues: 790 loop : -1.57 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 606 TYR 0.011 0.001 TYR B 607 PHE 0.016 0.002 PHE C 3 TRP 0.007 0.001 TRP A 227 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00228 (37730) covalent geometry : angle 0.55911 (50940) hydrogen bonds : bond 0.03311 ( 2160) hydrogen bonds : angle 4.19042 ( 6150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: D 201 PHE cc_start: 0.7261 (m-80) cc_final: 0.6567 (m-80) REVERT: D 269 MET cc_start: 0.7803 (mmp) cc_final: 0.7399 (mmm) REVERT: D 615 LEU cc_start: 0.9404 (pp) cc_final: 0.9195 (tp) REVERT: D 634 MET cc_start: 0.5521 (tmm) cc_final: 0.4849 (ppp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0483 time to fit residues: 1.4189 Evaluate side-chains 16 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 201 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 90 optimal weight: 0.0570 chunk 237 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 overall best weight: 1.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.038612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.030505 restraints weight = 53378.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.031327 restraints weight = 34415.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.031898 restraints weight = 25462.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.032287 restraints weight = 20595.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.032542 restraints weight = 17825.312| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 37730 Z= 0.104 Angle : 0.542 7.575 50940 Z= 0.275 Chirality : 0.039 0.144 6010 Planarity : 0.005 0.122 6610 Dihedral : 4.577 22.004 5050 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.66 (0.13), residues: 4820 helix: 2.41 (0.11), residues: 2110 sheet: -0.22 (0.17), residues: 790 loop : -1.61 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 271 TYR 0.010 0.001 TYR H 607 PHE 0.013 0.001 PHE E 3 TRP 0.011 0.002 TRP A 227 HIS 0.001 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00216 (37730) covalent geometry : angle 0.54217 (50940) hydrogen bonds : bond 0.03197 ( 2160) hydrogen bonds : angle 4.02618 ( 6150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 269 MET cc_start: 0.8103 (mmp) cc_final: 0.7587 (mmm) REVERT: G 308 MET cc_start: 0.8891 (mmp) cc_final: 0.8294 (mmm) REVERT: G 634 MET cc_start: 0.6204 (tmm) cc_final: 0.5487 (ptt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0724 time to fit residues: 2.1569 Evaluate side-chains 17 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 179 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 393 optimal weight: 1.9990 chunk 295 optimal weight: 0.0980 chunk 412 optimal weight: 7.9990 chunk 416 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.036964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028887 restraints weight = 52175.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029645 restraints weight = 34227.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030160 restraints weight = 25630.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.030500 restraints weight = 20964.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.030749 restraints weight = 18313.200| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37730 Z= 0.156 Angle : 0.614 9.842 50940 Z= 0.314 Chirality : 0.040 0.196 6010 Planarity : 0.005 0.099 6610 Dihedral : 4.674 21.488 5050 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.59 (0.13), residues: 4820 helix: 2.34 (0.11), residues: 2110 sheet: -0.22 (0.17), residues: 790 loop : -1.66 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 606 TYR 0.010 0.002 TYR B 607 PHE 0.015 0.002 PHE F 139 TRP 0.004 0.001 TRP D 614 HIS 0.000 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00323 (37730) covalent geometry : angle 0.61404 (50940) hydrogen bonds : bond 0.03539 ( 2160) hydrogen bonds : angle 4.28118 ( 6150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.70 seconds wall clock time: 40 minutes 17.02 seconds (2417.02 seconds total)