Starting phenix.real_space_refine on Tue Sep 15 08:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sih_10210/09_2026/6sih_10210.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sih_10210/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6sih_10210/09_2026/6sih_10210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sih_10210/09_2026/6sih_10210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sih_10210/09_2026/6sih_10210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sih_10210/09_2026/6sih_10210.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.48, 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 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: 1.14 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: 6.43 Time building geometry restraints manager: 4.20 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: 0.15 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.240 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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/Z covalent geometry : bond 0.00456 / 0.24 (37730) covalent geometry : angle 0.54402 / 0.33 (50940) hydrogen bonds : bond 0.15441 / 10.42 ( 2160) hydrogen bonds : angle 7.08063 / 4.82 ( 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 : 0.146 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: 0.0934 time to fit residues: 3.7806 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 : 0.122 ------------------------------------------------------------------------------- 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... A 99 GLN A 107 GLN A 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 = 0.3192 r_free = 0.3192 target = 0.038488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.030476 restraints weight = 50606.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.031365 restraints weight = 31284.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.031956 restraints weight = 22490.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.032351 restraints weight = 17930.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.032570 restraints weight = 15357.508| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1899 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 : 9.57 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 F 617 PHE 0.010 0.002 PHE J 384 TRP 0.008 0.001 TRP J 227 HIS 0.002 0.002 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (37730) covalent geometry : angle 0.63285 / 0.33 (50940) hydrogen bonds : bond 0.04693 / 3.18 ( 2160) hydrogen bonds : angle 5.44027 / 3.70 ( 6150) *********************** REFINEMENT MACRO_CYCLE 2 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 30 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: G 212 TYR cc_start: 0.8381 (m-10) cc_final: 0.7803 (m-80) REVERT: G 269 MET cc_start: 0.8301 (mmp) cc_final: 0.7905 (mmm) REVERT: G 378 MET cc_start: 0.4891 (ttt) cc_final: 0.4630 (ttt) REVERT: G 603 ILE cc_start: 0.8515 (mt) cc_final: 0.8070 (mt) REVERT: G 617 TYR cc_start: 0.6652 (p90) cc_final: 0.6161 (m-80) REVERT: G 624 LEU cc_start: 0.9017 (tt) cc_final: 0.8783 (mm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0582 time to fit residues: 2.3518 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 : 0.144 ------------------------------------------------------------------------------- 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: 0.0870 chunk 326 optimal weight: 0.0470 chunk 79 optimal weight: 6.9990 chunk 434 optimal weight: 0.8980 chunk 390 optimal weight: 8.9990 chunk 415 optimal weight: 6.9990 chunk 420 optimal weight: 0.2980 chunk 303 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 99 GLN G 107 GLN G 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 = 0.3209 r_free = 0.3209 target = 0.039437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031205 restraints weight = 49833.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032132 restraints weight = 31056.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.032731 restraints weight = 22791.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.033138 restraints weight = 18469.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033373 restraints weight = 15965.627| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2692 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= 0.114 Angle : 0.572 8.705 50940 Z= 0.298 Chirality : 0.040 0.162 6010 Planarity : 0.002 0.018 6610 Dihedral : 5.121 26.156 5050 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 0.19 (0.12), residues: 4820 helix: 1.66 (0.11), residues: 2040 sheet: -0.38 (0.16), residues: 810 loop : -1.31 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 606 TYR 0.012 0.001 TYR J 617 PHE 0.010 0.001 PHE I 139 TRP 0.006 0.001 TRP A 227 HIS 0.001 0.001 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (37730) covalent geometry : angle 0.57157 / 0.30 (50940) hydrogen bonds : bond 0.04113 / 2.80 ( 2160) hydrogen bonds : angle 5.05324 / 3.44 ( 6150) *********************** REFINEMENT MACRO_CYCLE 3 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 25 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: D 269 MET cc_start: 0.7652 (mmp) cc_final: 0.7073 (mmm) REVERT: D 603 ILE cc_start: 0.8663 (mt) cc_final: 0.8284 (mt) REVERT: D 617 TYR cc_start: 0.6925 (p90) cc_final: 0.6673 (m-80) REVERT: D 624 LEU cc_start: 0.9079 (tt) cc_final: 0.8876 (mm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0824 time to fit residues: 2.6456 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 : 0.151 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 403 optimal weight: 0.0670 chunk 196 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 389 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 424 optimal weight: 0.8980 chunk 314 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN D 99 GLN D 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 = 0.3215 r_free = 0.3215 target = 0.039508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031201 restraints weight = 50786.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032092 restraints weight = 32081.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.032689 restraints weight = 23644.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.033102 restraints weight = 19115.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033374 restraints weight = 16521.743| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 37730 Z= 0.103 Angle : 0.548 7.064 50940 Z= 0.287 Chirality : 0.040 0.200 6010 Planarity : 0.003 0.053 6610 Dihedral : 5.012 29.334 5050 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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 : 0.00 % 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: 0.45 (0.12), residues: 4820 helix: 1.92 (0.11), residues: 2040 sheet: -0.15 (0.17), residues: 810 loop : -1.27 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 606 TYR 0.012 0.001 TYR D 617 PHE 0.008 0.001 PHE C 415 TRP 0.006 0.001 TRP A 227 HIS 0.002 0.001 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (37730) covalent geometry : angle 0.54811 / 0.29 (50940) hydrogen bonds : bond 0.03775 / 2.57 ( 2160) hydrogen bonds : angle 4.80740 / 3.27 ( 6150) *********************** REFINEMENT MACRO_CYCLE 4 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 21 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: D 617 TYR cc_start: 0.7183 (p90) cc_final: 0.6904 (m-10) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0746 time to fit residues: 2.1059 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 : 0.154 ------------------------------------------------------------------------------- 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: 8.9990 chunk 376 optimal weight: 0.0980 chunk 111 optimal weight: 7.9990 chunk 397 optimal weight: 0.0060 chunk 335 optimal weight: 0.9980 chunk 406 optimal weight: 1.9990 chunk 404 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 462 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 438 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.039490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031141 restraints weight = 50531.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.031972 restraints weight = 32991.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.032557 restraints weight = 24526.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032956 restraints weight = 19983.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033187 restraints weight = 17284.623| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37730 Z= 0.104 Angle : 0.556 6.733 50940 Z= 0.286 Chirality : 0.040 0.142 6010 Planarity : 0.005 0.106 6610 Dihedral : 4.834 24.341 5050 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 0.75 (0.13), residues: 4820 helix: 2.08 (0.11), residues: 2110 sheet: 0.08 (0.17), residues: 790 loop : -1.16 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 32 TYR 0.012 0.001 TYR H 617 PHE 0.009 0.001 PHE I 139 TRP 0.009 0.002 TRP D 614 HIS 0.001 0.001 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (37730) covalent geometry : angle 0.55597 / 0.29 (50940) hydrogen bonds : bond 0.03626 / 2.47 ( 2160) hydrogen bonds : angle 4.36065 / 3.02 ( 6150) *********************** REFINEMENT MACRO_CYCLE 5 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 19 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 269 MET cc_start: 0.7014 (mmm) cc_final: 0.6405 (mmm) REVERT: D 634 MET cc_start: 0.5618 (tmm) cc_final: 0.4949 (ppp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0627 time to fit residues: 1.7127 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 : 0.152 ------------------------------------------------------------------------------- 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: 0.9990 chunk 467 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 312 optimal weight: 10.0000 chunk 434 optimal weight: 0.8980 chunk 216 optimal weight: 0.0000 chunk 316 optimal weight: 0.0870 chunk 233 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 372 optimal weight: 0.3980 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.039737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031377 restraints weight = 50680.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.032216 restraints weight = 33050.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.032795 restraints weight = 24671.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.033191 restraints weight = 20158.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.033458 restraints weight = 17563.351| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37730 Z= 0.115 Angle : 0.556 8.416 50940 Z= 0.285 Chirality : 0.043 0.341 6010 Planarity : 0.003 0.038 6610 Dihedral : 4.727 23.510 5050 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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: 0.90 (0.13), residues: 4820 helix: 2.26 (0.11), residues: 2110 sheet: 0.09 (0.17), residues: 790 loop : -1.11 (0.16), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 606 TYR 0.030 0.002 TYR H 617 PHE 0.008 0.001 PHE J 295 TRP 0.012 0.002 TRP J 614 HIS 0.001 0.001 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (37730) covalent geometry : angle 0.55584 / 0.29 (50940) hydrogen bonds : bond 0.03488 / 2.37 ( 2160) hydrogen bonds : angle 4.28760 / 2.98 ( 6150) *********************** REFINEMENT MACRO_CYCLE 6 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 20 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 269 MET cc_start: 0.7067 (mmm) cc_final: 0.6408 (mmm) REVERT: D 628 LEU cc_start: 0.8963 (mm) cc_final: 0.8741 (pp) REVERT: D 634 MET cc_start: 0.5611 (tmm) cc_final: 0.5103 (ppp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0608 time to fit residues: 1.7332 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 ------------------------------------------------------------------------------- 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: 8.9990 chunk 184 optimal weight: 0.0050 chunk 289 optimal weight: 0.0670 chunk 297 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 445 optimal weight: 10.0000 chunk 394 optimal weight: 0.4980 chunk 417 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 204 optimal weight: 0.0970 chunk 186 optimal weight: 0.3980 overall best weight: 0.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.040392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.031944 restraints weight = 51146.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.032817 restraints weight = 32861.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.033395 restraints weight = 24385.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.033792 restraints weight = 19849.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034071 restraints weight = 17222.970| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 37730 Z= 0.100 Angle : 0.536 8.402 50940 Z= 0.270 Chirality : 0.039 0.132 6010 Planarity : 0.002 0.021 6610 Dihedral : 4.547 24.629 5050 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 1.03 (0.13), residues: 4820 helix: 2.46 (0.11), residues: 2110 sheet: 0.09 (0.17), residues: 790 loop : -1.15 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 606 TYR 0.009 0.001 TYR E 617 PHE 0.007 0.001 PHE A 295 TRP 0.008 0.002 TRP B 614 HIS 0.001 0.001 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (37730) covalent geometry : angle 0.53576 / 0.27 (50940) hydrogen bonds : bond 0.03132 / 2.12 ( 2160) hydrogen bonds : angle 4.02611 / 2.81 ( 6150) *********************** REFINEMENT MACRO_CYCLE 7 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 19 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: D 117 LYS cc_start: 0.6704 (mptt) cc_final: 0.6376 (mmtp) REVERT: D 269 MET cc_start: 0.7307 (mmm) cc_final: 0.6747 (mmm) REVERT: D 378 MET cc_start: 0.4384 (ttt) cc_final: 0.4102 (ttt) REVERT: D 634 MET cc_start: 0.5629 (tmm) cc_final: 0.5188 (ptt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0647 time to fit residues: 1.7559 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 : 0.161 ------------------------------------------------------------------------------- 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: 0.0170 chunk 166 optimal weight: 0.0270 chunk 463 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 107 optimal weight: 0.0030 chunk 359 optimal weight: 10.0000 chunk 387 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 360 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 385 optimal weight: 8.9990 overall best weight: 0.1698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.040111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.031473 restraints weight = 50728.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032279 restraints weight = 33915.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.032829 restraints weight = 25716.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.033215 restraints weight = 21264.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.033473 restraints weight = 18624.566| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37730 Z= 0.096 Angle : 0.512 7.065 50940 Z= 0.260 Chirality : 0.039 0.138 6010 Planarity : 0.002 0.022 6610 Dihedral : 4.346 23.527 5050 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.14 (0.13), residues: 4820 helix: 2.55 (0.11), residues: 2110 sheet: 0.19 (0.17), residues: 790 loop : -1.11 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 271 TYR 0.016 0.001 TYR A 617 PHE 0.007 0.001 PHE C 295 TRP 0.010 0.001 TRP G 227 HIS 0.002 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (37730) covalent geometry : angle 0.51218 / 0.26 (50940) hydrogen bonds : bond 0.03089 / 2.09 ( 2160) hydrogen bonds : angle 3.91209 / 2.74 ( 6150) *********************** REFINEMENT MACRO_CYCLE 8 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 18 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: D 117 LYS cc_start: 0.6647 (mptt) cc_final: 0.6333 (mmtp) REVERT: D 262 PHE cc_start: 0.7839 (m-80) cc_final: 0.7532 (m-80) REVERT: D 269 MET cc_start: 0.7304 (mmm) cc_final: 0.7035 (mmm) REVERT: D 634 MET cc_start: 0.5978 (tmm) cc_final: 0.5635 (ptt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0669 time to fit residues: 1.7199 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 388 optimal weight: 0.9980 chunk 436 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 404 optimal weight: 9.9990 chunk 446 optimal weight: 0.0570 chunk 297 optimal weight: 0.0770 chunk 154 optimal weight: 0.0970 chunk 418 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 255 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.039810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.031525 restraints weight = 50806.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.032351 restraints weight = 33160.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.032922 restraints weight = 24585.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.033312 restraints weight = 19909.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.033576 restraints weight = 17176.876| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37730 Z= 0.090 Angle : 0.488 7.109 50940 Z= 0.246 Chirality : 0.038 0.128 6010 Planarity : 0.002 0.022 6610 Dihedral : 4.144 22.368 5050 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: 1.40 (0.13), residues: 4820 helix: 2.85 (0.11), residues: 2110 sheet: 0.34 (0.17), residues: 790 loop : -1.09 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 606 TYR 0.010 0.001 TYR C 617 PHE 0.008 0.001 PHE H 138 TRP 0.008 0.001 TRP D 227 HIS 0.001 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (37730) covalent geometry : angle 0.48824 / 0.25 (50940) hydrogen bonds : bond 0.02777 / 1.87 ( 2160) hydrogen bonds : angle 3.72415 / 2.61 ( 6150) *********************** REFINEMENT MACRO_CYCLE 9 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 20 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 269 MET cc_start: 0.7411 (mmm) cc_final: 0.7132 (mmm) REVERT: G 308 MET cc_start: 0.8809 (mmp) cc_final: 0.8231 (mmm) REVERT: G 378 MET cc_start: 0.3811 (ttt) cc_final: 0.3546 (ttt) REVERT: G 634 MET cc_start: 0.6106 (tmm) cc_final: 0.5877 (ptt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0734 time to fit residues: 2.0280 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 : 0.154 ------------------------------------------------------------------------------- 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: 0.0670 chunk 230 optimal weight: 0.0020 chunk 203 optimal weight: 8.9990 chunk 333 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 97 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.040191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.031739 restraints weight = 52595.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.032620 restraints weight = 34055.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.033225 restraints weight = 25155.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.033629 restraints weight = 20250.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.033916 restraints weight = 17415.055| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37730 Z= 0.088 Angle : 0.499 7.264 50940 Z= 0.249 Chirality : 0.039 0.129 6010 Planarity : 0.002 0.022 6610 Dihedral : 4.137 22.326 5050 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: 1.44 (0.13), residues: 4820 helix: 3.06 (0.11), residues: 2050 sheet: 0.46 (0.18), residues: 790 loop : -1.21 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 271 TYR 0.014 0.001 TYR D 617 PHE 0.014 0.001 PHE E 3 TRP 0.013 0.002 TRP B 227 HIS 0.002 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 (37730) covalent geometry : angle 0.49875 / 0.25 (50940) hydrogen bonds : bond 0.02809 / 1.89 ( 2160) hydrogen bonds : angle 3.69647 / 2.59 ( 6150) ********************** REFINEMENT MACRO_CYCLE 10 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 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: G 269 MET cc_start: 0.7450 (mmm) cc_final: 0.7060 (mmm) REVERT: G 308 MET cc_start: 0.8860 (mmp) cc_final: 0.8250 (mmm) REVERT: G 378 MET cc_start: 0.3823 (ttt) cc_final: 0.3325 (ttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0627 time to fit residues: 1.7134 Evaluate side-chains 15 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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: 0.9980 chunk 239 optimal weight: 0.7980 chunk 28 optimal weight: 0.0000 chunk 218 optimal weight: 1.9990 chunk 393 optimal weight: 0.9990 chunk 295 optimal weight: 4.9990 chunk 412 optimal weight: 0.0570 chunk 416 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.040071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.031712 restraints weight = 51234.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.032567 restraints weight = 33293.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.033158 restraints weight = 24616.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.033565 restraints weight = 19868.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.033847 restraints weight = 17076.979| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37730 Z= 0.091 Angle : 0.509 7.094 50940 Z= 0.260 Chirality : 0.039 0.134 6010 Planarity : 0.003 0.060 6610 Dihedral : 4.062 21.977 5050 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.46 (0.13), residues: 4820 helix: 3.03 (0.11), residues: 2050 sheet: 0.51 (0.17), residues: 790 loop : -1.17 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.006 0.001 TYR C 617 PHE 0.012 0.001 PHE J 3 TRP 0.012 0.001 TRP D 227 HIS 0.002 0.001 HIS H 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (37730) covalent geometry : angle 0.50900 / 0.26 (50940) hydrogen bonds : bond 0.02849 / 1.92 ( 2160) hydrogen bonds : angle 3.72868 / 2.61 ( 6150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.11 seconds wall clock time: 43 minutes 47.60 seconds (2627.60 seconds total)